Functional Specifications - Chromeleon 7.2.10

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Functional Specifications
Chromeleon 7.2.10 • May 2019
Chromeleon 7
Copyright
For Research Use Only. Not for use in diagnostic procedures.
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Functional Specifications
Chromeleon 7
Table of Contents
Contents
Table of Contents i
1 About this Document 7

1.1 Scope 7
1.2 Other Documentation 7
2 Overview of System 8
3 Chromeleon Console 9
3.1 Menu Bar 10
3.1.1 Station Qualification 11
3.1.2 Instrument Qualification 11
3.1.3 Custom Variables Editor 11
3.1.4 Custom Formulas Editor 12
3.1.5 Administration Console 12
3.1.6 Preferences 13
3.1.7 Virtual Column Separation Simulator 13
3.1.8 Import 14
3.2 Instruments Category 15
3.2.1 Instruments Category Bar 15
3.2.2 Instrument Queue 23
3.2.3 Instrument Audit Trail 24
3.3 Data Category 25
3.3.1 Sequence Status Bar 26
3.3.2 Sequence Toolbar 27
3.3.3 Sequence Table Context Menu 28
3.3.4 Sequence Context Menu 29
3.4 eWorkflows Category 30
3.4.1 Editing an eWorkflow 30
3.5 Command Line Parameters 34
4 Objects in the Data Category 36

4.1 Data Vaults 36
4.1.1 Data Vault Properties 36
4.1.2 General 36
4.1.3 Access Control 36
4.1.4 Downtime 36
4.1.5 Database Statistics 37
4.1.6 Raw Data Statistics 37
4.2 Folders 37
4.2.1 General 37
4.2.3 Raw Data Statistics 37
4.3 Sequences 37
4.3.1 Injection List 38
4.3.2 Sequence Properties 40
4.3.3 Injection Rack View 41
Functional Specifications Page i

Chromeleon 7
4.4 Injection Query 42

4.5 Deleted Items 42
4.6 Instrument Method 42
4.6.1 DAD-3000(RS) 42
4.6.2 Mass Spectrometers 44
4.6.3 Startup / Shutdown 44
5 Chromatography Studio 46
5.1 Studio Button 46
5.2 View Settings 47
5.3 Processing Method 48
5.3.1 Detection 49
5.3.2 Component Table 52
5.3.3 Calibration 63
5.3.4 Peak Group Table 63
5.3.5 Chromatogram Subtraction 64
5.3.6 UV Spectral Library Screening 64
5.3.7 SST/IRC 66
5.3.8 Advanced Settings 71
5.3.9 Composite Scoring 71
5.3.10 MS Detection 72
5.3.11 MS Settings 74
5.3.12 MS Library Screening 75
5.3.13 Peptide Table 76
5.3.14 QD Calibration 76
5.3.15 MS Component Table Import 77
5.3.16 MS Component Table Export 77
5.3.17 Cobra Wizard 80
5.3.18 SmartPeaks 80
5.3.19 Component Table Wizard 81
5.3.20 Layouts 82
5.4 Data Processing Category 82
5.4.1 Chromatogram Pane 83
5.4.2 Calibration Plot Pane 98
5.4.3 Peak Properties Pane 101
5.4.4 Interactive Charts Pane 103
5.4.5 Contour/3D Plot 109
5.4.6 UV-Vis Spectra Pane 114
5.4.7 Fluorescence Spectra Pane 122
5.4.8 I-t Plot Pane 127
5.4.9 Interactive Results Pane 131
5.4.10 Injection Rack Pane 132
5.4.11 Fraction Tray Pane 133
5.4.12 Mass Spectrum Pane 134
5.4.13 MS Components Pane 144
5.4.14 Tentatively Identified Peaks Pane 152
5.4.15 MS AutoFilters Pane 152
5.4.16 SmartLink 156
5.4.17 On-Demand View Updating 158
5.5 Non-Targeted MS Processing Category 158
5.5.1 Ribbon Bar 158
5.5.2 Processing Pane 159
5.5.3 Frame Plot Pane 160
Page ii Functional Specifications

Chromeleon 7
5.5.4 Frame Report Pane 162

5.5.5 Chromatogram Plot Pane 162
5.5.6 Mass Spectra Pane 163
5.5.7 Processing Parameters Pane 163
5.6 Intact Protein Deconvolution Category 163
5.6.1 Ribbon Bar 163
5.6.2 Processing Method Pane 164
5.6.3 Processing Parameters Pane 167
5.6.4 Component Results Pane 167
5.6.5 Chromatogram Pane 169
5.6.6 Deconvoluted Spectrum Pane 173
5.6.7 Source Spectrum Pane 176
5.7 Report Template 179
5.7.1 Chromatogram Plot 180
5.7.2 Calibration Plot 187
5.7.3 UV-Vis Spectra Plot 189
5.7.4 Contour Plot 194
5.7.5 Mass Spectrum Plot 195
5.7.6 MS Components Plot 201
5.7.7 Injection Rack View 206
5.7.8 Fraction Tray Plot 207
5.7.9 Fluorescence Spectra Plot 208
5.7.10 I-t Plot 212
5.7.11 NTMS Frame Plot 217
5.7.12 NTMS Processing Parameters Table 218
5.7.13 IPD Chromatogram Plot 219
5.7.14 IPD Mass Deconvoluted Spectra Plot 223
5.7.15 IPD Mass Source Spectra Plot 226
5.7.16 IPD Processing Parameters Table 228
5.7.17 Result/Scatter Charts 228
5.7.18 General Charts 234
5.7.19 Illustrations 234
5.7.20 Chromeleon Report Tables 235
5.7.21 Chromeleon Report Variables 260
5.7.22 Spreadsheet Formula 261
5.7.23 Page Setup 264
5.7.24 Autorepeat Areas 265
5.7.25 Protection 269
5.7.26 Check for Errors 269
5.7.27 Custom Formulas 269
5.8 Electronic Reports 271
5.8.1 Creation Settings 271
5.9 Spectral Library 272
5.10 MS Spectral Library 273
5.11 Data Audit Trail 274
5.12 Injection Audit Trail 276
6 Versioning 278
7 Chromeleon Variables 279

7.1 Global Functions 279
7.2 General 279
7.3 Sequence 279
7.4 Injection 284
Functional Specifications Page iii

Chromeleon 7
7.5 Audit Trail 286

7.5.1 HPG-3200RS Pump Audit Trail Variables 286
7.5.2 DAD-3000(RS) 287
7.6 Preconditions 287
7.7 Data Audit Trail 287
7.8 Chromatogram 287
7.8.1 Standard Variables 288
7.9 MS Signal Extraction Parameters 291
7.10 Peak Results 291
7.11 Peak Calibration 296
7.12 Peak Purity and Identification 300
7.13 Composite Scoring (Peak Purity and Identification) 301
7.14 FL Spectrum 301
7.15 Hit Mass Spectrum 302
7.16 Mass Spectrum 302
7.17 UV Spectrum 303
7.18 Hit Spectrum 303
7.19 Peak Tentative Identification 305
7.20 Processing Method 305
7.21 Composite Scoring (Processing Method) 309
7.22 MS Library Screening 310
7.23 MS Settings 310
7.24 System Suitability Test Case Details 311
7.25 Spectral Library Screening Parameters 311
7.26 UV Spectra Settings 311
7.27 Detection Parameters 312
7.28 Component 312
7.29 Peak Group 312
7.30 Instrument Method 312
7.31 Mass Spectrometry 314
7.32 MS Device 314
7.33 MS Detection Parameters 314
7.34 Peptide 315
7.35 Isotope 316
7.36 Non-Targeted MS Processing 316
7.37 Intact Protein Deconvolution 317
7.38 Frame 320
7.39 Report Template 320
7.40 eWorkflow 322
8 Electronic Signatures 323

8.1 Submit Signature 323
8.2 Review Signature 323
8.3 Approve Signature 324
8.4 Remove Signature 324
8.5 Verify Report 324
8.6 Report Signed results 324
9 Chromeleon Services Manager 325

9.1 Instrument Controller Service 325
9.2 Other Chromeleon services 325
10 Instrument Configuration Manager 326

10.1 Properties 326
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Chromeleon 7

10.1.2 Queue Settings 326
11 Administration Console 328

11.1 License Manager 328
11.1.1 Client Licenses 328
11.1.2 Instrument Controller Licenses 329
11.1.3 License Overview 329
11.2 Scheduler 329
11.2.1 Scheduler (Chromeleon Domain) 330
11.3 User Database 331
11.3.1 Toolbar 331
11.3.2 User Database Policies 332
11.3.3 Chromeleon Users 334
11.3.4 User Properties 335
11.3.5 Access Groups 336
11.3.6 Roles 337
11.3.7 Audit Trail 341
11.4 Global Policies 341
11.4.1 Toolbar 341
11.4.2 User Mode 341
11.4.3 Host Name Resolution 341
11.4.4 Multi-User Logon 342
11.4.5 Injection Locking 342
11.4.6 Remote Data Vaults 342
11.4.7 Instrument Audit Trails 342
11.4.8 Detection Algorithm Version 342
11.4.9 User Templates Location 342
11.4.10 Watermark 343
11.4.11 UI Customizations 343
11.4.12 Privileged Actions 343
11.4.13 Email Configuration 343
11.4.14 Station Audit 343
11.4.15 License 343
11.4.16 Raw Data 344
11.5 Define Policies in Organizational Units 344
11.5.1 Separate Policy Settings for Organizational Units 344
11.5.2 Use <Global> Settings 344
11.6 eWorkflow Tags 344
11.6.1 Toolbar 344
11.6.2 Create New Tag 345
11.7 Domain Resources 345
11.7.1 All Resources 345
11.7.2 Computers 346
11.7.3 Data Vaults 347
11.7.4 Instruments 348
11.7.5 Chromeleon Consoles 348
11.7.6 System Printers 348
11.8 Local Machine 348
11.8.1 Manage Data Vaults 349
11.9 Configure Discovery 351
11.9.1 Discovery Configuration 351
12 Administrative Audit Trails 352
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Chromeleon 7
13 Time Zone Information 353
14 Changes Introduced in Version 354

14.1 7.2 354
14.2 7.2 SR1 355
14.3 7.2 SR2 356
14.4 7.2 SR3 356
14.5 7.2 SR5 358
14.6 7.2.6 358
14.7 7.2.7 359
14.8 7.2.8 359
14.9 7.2.9 359
14.10 7.2.10 360
Page vi Functional Specifications

Chromeleon 7
1 About this Document

This document details the functions available in ChromeleonTM 7.2.10. Every effort has been made to provide details of all
functionality.
The blue text in the document describes functionality introduced in the current Chromeleon version, the black text describes
functionality previously available.
1.1 Scope
The functional specifications cover all functions available in version 7.2.10 of the Chromeleon software. The document will
be updated for future main versions of Chromeleon, including service releases.
1.2 Other Documentation

There are a number of other documents available that will help you to learn more about Chromeleon. The documents are
available in electronic form on the installation disk in the Documents folder.
Functional Specifications Page 7

Chromeleon 7
2 Overview of System
Thermo Scientific™ Dionex™ Chromeleon™ 7 Chromatography Data System (“Chromeleon“) is a PC software package
for chromatography instrument control, data acquisition, data management and reporting. It is designed for Windows
Operating Systems and has the following main features:
• True Client/server architecture for data acquisition and instrument control; support of all common network
protocols;
• True 32-bit algorithms guarantee high processing speed and maximum system stability;
• Access to data via a network allows sharing of data between different laboratories and/or different company sites;
• Easy-to-use user interface with a Microsoft Outlook style Console and spreadsheet-based Report Designer;
• Context sensitive help functions and comprehensive Quick Start Guide;
• Provides instrument control HPLC, GC, IC and MS instruments;
• Uniform user interface and operation, independent from operating system and connected chromatographs;
• GLP/GMP and 21 CFR part 11 compliant audit trails/history; documentation of all events and user actions;
• Proven algorithms for virtually parameter-free, automatic integration of difficult chromatograms;
• Unique SmartPeaks tool for fast and easy integration of unresolved peaks;
• Workflow management via eWorkflows tool;
• Dynamic data processing for fast and efficient optimization of the integration, calibration and reports;
• Integrated relational database for efficient management and fast access to data; flexible database concept with
support for MS-SQL-Express and/or MS-SQL-Server databases and Oracle databases;
• Powerful chromatography data-mining tools for fast evaluation of chromatographic results; more than 130
variables are available for queries on the relational database; report templates can be directly linked to a query;
• Excel-like spreadsheet Report Designer; custom calculations, formulas and charts;
• User management for the administration and tuning of user privileges, access rights, and so on.
Page 8 Functional Specifications

Chromeleon 7
3 Chromeleon Console
The Chromeleon console is the user interface for accessing all major aspects of a Chromeleon installation. It is designed to
look like Microsoft Outlook. The figure below shows an example of the browser window and also shows all the main
Chromeleon file types.
Figure 1: Overview of the Chromeleon console
1. Category Bars – These provide direct access to
a. Instruments (see section 3.2)
b. Data (see section 3.2.3)
c. eWorkflows (see section 3.4)
2. Navigation Area – This displays all objects associated with a specific category bar. Details are provided in the
relevant section for the category bars.
3. Work Area – This displays details about the selected object in the navigation area. More details are provided in
the relevant section for the category bars.
4. The Filter Toolbar offers different views of the list in the Navigation Pane:
a. Local: Items available on the local Chromeleon station.
b. Global: Items available on the Chromeleon Domain.
c. Favorites: Items that have been designated as favorites.
d. Custom: Filter based on text input.
5. Menu Bar – provides major commands relevant to the console (see section 3.1).
6. The Sequence Toolbar is available when a Sequence is selected in the Navigation Pane.
7. The Sequence Status Bar indicates the sequence status.
8. Status Bar shows general information such as the currently logged on user and role.

Chromeleon 7
3.1 Menu Bar

The following options are available from the menu tool bar:
Function Sub Function Description

Navigation Buttons Go Back One step back in the navigation history
Go Forward One step forward in the navigation history
Create Button Folder Creates a new folder
Sequence Creates a new sequence
Sequence from Worklist Creates a new sequence from a LIMS Worklist
Instrument Method Creates a new instrument method
Processing Method Creates a new processing method
Report Template Creates a new report template
Injection Query Creates a new injection query
Spectral Library Creates a new spectral library
View Settings Creates a new view setting
eWorkflow Creates a new eWorkflow
Electronic Report Creates a new electronic report
File Send To Creates an external file (.cmbx) containing all selected
objects. This file can be used to transfer data from one
Chromeleon 7 installation to another.
Two formats; Chromeleon data files (*.cmbx) which
corresponds to the v2.0 format. The v1.0 format is
represented by Chromeleon 7.0 – 7.2 SR2 data files (*.
cmbx)
Import Allows the importing of Chromeleon data and Non-
Chromeleon data (see 3.1.8).
Save As Allows the selected object to be saved under a different
name
Lock Client Manually locks the Chromeleon client
Exit Exits Chromeleon
Edit Undo Undoes previous command
Redo Repeats previous command
Cut Prepares selected object for a move operation
Copy Copies the selected object to the clipboard
Paste Pastes the selected object (moves an object that has
previously been selected as Cut)
Rename Allows renaming of an object
Delete Deletes the selected object
View Instruments Switch to the Instrument category
Data Switch to the Data category
eWorkflows Switch to the eWorkflows category
Refresh Refresh the on-screen display
Tools Station Qualification See 3.1.1
Instrument Qualification See 3.1.2
Custom Variables Editor See 3.1.3
Custom Formulas Editor See 3.1.4
Administration Console See 3.1.5
Preferences See 3.1.6

Chromeleon 7

Virtual Column Separation See 3.1.7
Simulator
Help Index Opens Chromeleon Client Help file
About Chromeleon Allows viewing of information about the Chromeleon
installation including the license key serial number
3.1.1 Station Qualification

Station Qualification allows users to run either the Chromeleon IQ or Chromeleon OQ or Chromeleon PQ.
The automated Installation Qualification (IQ) procedure checks if all relevant files required by Chromeleon have been
installed correctly.
The automated Operational Qualification procedure checks that Chromeleon correctly calculates data. A data set is
imported in to Chromeleon, integrated and then processed. The data set report contains the expected values and the values
calculated by Chromeleon. These values must match in order for Chromeleon to report the OQ has passed.
The automated Performance Qualification (PQ) analyzes the performance of your Chromeleon installation. It will provide a
report on the performance measurements and an assessment of observed values in comparison to standard Chromeleon
installations or previously executed performance qualification runs.
The following Components for Performance Qualification are available:
Parameter Description
Discovery This test provides and removes temporary data and measures the according
timings.
User Management This test performs actions on the user database, e.g. create/delete user. The
Manage User Database privilege is required.
Licensing The time necessary for license retrieval on your workstation is analyzed.
Instrument Control Four different sequences are tested:
•empty sequences with 10 injections
•sequences with raw data in 10 injections
•sequences with raw data in 100 injections
•sequences with 3D data in 10 injections
This test performs actions on the instrument, e.g. launch an eWorkflow, add a
sequence to queue.
Data Vault You can verify whether the newly created data vault is suitable and identify
problems in existing data vaults. Empty sequences, sequences with raw data and
sequences with 3D data are tested. The same sequences are tested as for the
Instrument Control component. The actions performed for the respective
component during Performance Qualification represent typical user actions. Each
action is labelled with a weight which indicates the importance of its action. Each
action is repeated several times to obtain an average for the duration of each
action. This test performs typical actions on a data vault, such as create a
directory, import or copy a sequence etc..
3.1.2 Instrument Qualification

The automated Instrument Qualification procedure allows for automatically running the installation qualification (IQ), the
operational qualification (OQ), and the performance qualification (PQ).
3.1.3 Custom Variables Editor

This allows for the creation or import of custom variables for the sequence, injection list, and the component table in the
processing method. The following options are available:
Variable Sub Function Description

Name N/A Name of custom variable.
Context N/A The object the variable will be applied to. This can be
Sequence, Injection, or Component.

Chromeleon 7

Value Type Text Any combination of text and numeric characters can be
entered. The following properties can also be set:
•Empty values are Allowed
•Maximum length
•Default value
Numeric Numerical values can be stored. The following properties can
be applied:
•Default
•Maximum
•Minimum
•Precision
•Units
Date and Time Only date and time values can be entered or allow empty
values.
List Provides a selection list for the user to choose from. The
following properties can be set:
•Default
•List items
Description N/A Description of the custom variable.
Add Create a new custom variable Creates a new custom variable with unique properties.
Import a custom variable from a Imports a custom variable from the selected data vault.
data vault
Import a custom sequence Imports a custom sequence variable from the selected
variable from a sequence sequence.
Import a custom injection variable Imports a custom injection variable from the selected
from a sequence sequence.
Import a custom component Imports a custom component variable from the selected
variable from a processing method processing method.
Delete N/A Delete custom variables from list.
3.1.4 Custom Formulas Editor

This allows for the creation of custom formula templates for the data vault. The user then imports an instance into any
sequence. The following options are available:

Name N/A Name of custom formula.
Description N/A Free text description of custom formula
Formula N/A Any combination of Chromeleon variables from section 7 can
be entered
Header N/A Defines the report column header.
Unit N/A Defines the unit.
Format N/A Defines the number or date format for displaying results.
Add New Custom Formula Create a new custom formula Create a new custom formula with unique properties.
Import a custom formula template Import a custom formula template from the selected data
from a data vault vault.
Import a custom formula from a Import a custom formula from the selected sequence.
sequence
3.1.5 Administration Console

The Chromeleon Administration Console is a central access point for administrative tasks (see section 11).

Chromeleon 7
3.1.6 Preferences
This allows for setting general Chromeleon preferences to specify what occurs when you drag items between folders.

When dragging items between Ask Chromeleon will ask each time what to do with the selected
folders: item.
Copy Chromeleon will automatically copy from the source to the
destination folder.
Move Chromeleon will automatically move from the source to the
destination folder.
3.1.7 Virtual Column Separation Simulator

The Virtual Column Separation Simulator is a tool that uses known ion chromatographic retention data to predict new
retention data and chromatograms on the most popular Dionex anion-exchange and cation-exchange columns. The known
retention data were acquired at Dionex using an appropriate experimental design and then embedded into Virtual Column.
Figure 2 below shows the Virtual Column Separation Simulator interface.
A B
Figure 2: Virtual Column Separation Simulator

The following options can be set for the Separation Simulator (Figure 2A):
Function Description
Reset All Resets all data entries to blank.
Analyte Category Drop-down list of available analyte categories:
•Anions
•Cations
•Carbohydrates
Response By Drop-down list of following categories:
•Peak Area
•Concentration (mg/L)
•Concentration (mM)
Inj. Volume Edit Box to change the Injection Volume. Only available after selecting the
Concentration option for Response By.
Analytes Allows the user to select the analytes of interest.
Results Displays the separation results of the analytes of interest.

Chromeleon 7
Column Types Allows the user to select the column type:
•Standard Bore (4 mm & 5 mm ID)
•Microbore (2 mm & 3 mm ID)
•Capillary (<1 mm ID)
Methodologies Allows the user to select the methodology of interest:
•Carbonate – Isocratic
•Hydroxide – Gradient
•Hydroxide – Isocratic
•MSA – Isocratic
• MSA – Gradient
Column Selection Allows the user to select a specific column.
Temperature Allows the user for some columns to select a temperature and view the effect on the
separation.
Gradient Start Allows the user to select an eluent concentration at the beginning of the gradient from
a drop-down box, after selecting a column for a gradient simulation.
Flow rate Allows the user to define a flow rate.
Void Volume Allows the user to define a void volume.
For the Resolution Response Surface and Virtual Chromatogram (Figure 2B) the following

Optimize for Critical Pairs Optimizes separation for the critical peak pair.
All Analytes Optimizes separation for all analytes.
Selected Analyte Optimizes separation for selected analyte.
Eluent Preparation N/A Provides detailed instructions for eluent preparation
corresponding to the currently selected conditions. This option
is available only when an isocratic simulation is selected.
Fast Separation Resolution N/A Allows user to set minimum resolution required for fast
separations.
3.1.8 Import
3.1.8.1 Chromeleon Data

• Imports single Chromeleon data files of type:
• Chromeleon 7 data file (*. cmbx)
• Chromeleon 6 data files (*.cmb)
• Chromeleon eWorkflow files (*. ewfx)
• Chromeleon ePanel files (*. panx)
3.1.8.2 Bulk Import

Imports multiples of Chromeleon data files and also non-Chromeleon data from an external location to Chromeleon. Here
you can add files and folders for import, sort them, and adjust their import settings. You can also drag and drop files for
import into the left pane of the External Data Import dialog box.
Supported files types:
• Chromeleon 7 data file (*. cmbx)
• Chromeleon 6 data files (*.cmb)
• AnDI file (*.cdf)
• GAML file (*. gaml)
• Xcalibur Raw Data (*.raw)
• Xcalibur Sequence File (*.sld)

Chromeleon 7
• Atlas Workbook (*.ana)

• ChemStation Data files (.D)
3.1.8.3 ChemStation Method files (.M)

• ChemStation Signal files (.CH) (16 and 32 bit)
• ChemStation UV Spectral Data files (.UV) (16 and 32 bit)
• ChemStation Data Analysis Register files (.REG) (16 bit)
• ChemStation Sequence Template files (.S) (16 bit)
• ChemStation Batch files (.B) (16 bit)
• ChemStation Comma-Separated Values format files (.CSV) (16 bit)
• ChemStation Spectral Libraries (.UVL) (16 bit)
• Empower 2D data
• Empower 3D data
• Empower Instrument Methods
• Empower Processing Methods
The following options can be set for the Bulk Data Import:
Add Files and folders are added to the left pane and are listed in a tree view.
Remove To remove a file or folder from the list.
Sort grouped files Sort grouped files (e.g., several Xcalibur Raw Data files: *.raw), with the options:
• Move Up to move the selected files up the order in the list.
• Move Down to move the selected files down the order in the list.
• Sort by Acquisition Date/Time to sort the files by acquisition time and date
3.2 Instruments Category

3.2.1 Instruments Category Bar
Selecting the instruments category bar changes the contents in the navigation area to a list of all instruments registered on
the discovery server. The work area displays the ePanel Sets for the selected instrument (see Figure 3 below).

Chromeleon 7
Figure 3: Console view when the instruments category bar is selected

A. List of instruments in the navigation area that can be sorted by Locals, All, Favorites or by filtered by free text entry.
B. ePanel tabs providing direct access to the control options for individual modules (e.g. pump, sampler, etc.).
C. The Audit tab is always available and shows the instrument audit trail (see section Error! Reference source not
found.).
D. The Startup tab is available for instruments supporting Smart Startup and shows the instrument’s status during startup.
E. The Queue tab is always available and shows the list of sequences queued for analysis. Also, automatic instrument
startup, shutdown and standby can be activated here.
The following functions are always offered for all instruments in the toolbar:

Launch eWorkflow N/A Select eWorkflows associated with currently selected
instruments and runs eWorkflow wizard.
Smart Startup Using Queue Settings Starts up an instrument with the instrument method of the first
idle injection (that has an instrument method) in the first
sequence that is not finished.
Using Instrument Method Starts up an instrument with settings specified in a selected
instrument method.
Smart Shutdown Smart Shutdown Shuts down an instrument.
Smart Standby Sets the instrument to standby mode so that an instrument
can be re-activated quickly. A minimum flow is retained.
Take Control N/A Allows a user to take control of an instrument.
Monitor Baseline Monitor Baseline Starts a baseline monitor for each channel you select to
monitor.
Stop Stops baseline monitoring and saves the monitor baseline
data in the Manual sequence

Chromeleon 7

Stop and Save Stops baseline monitoring and appends the data to the
sequence specified in the Monitor Baseline Save Preferences
dialog box.
Stop and Save As Stops baseline monitoring and opens a dialog box for you to
specify either a new sequence or an existing sequence in
which to save the data.
Preferences Define a preference for which monitor save action is preferred;
Stop, Stop and Save or Stop and Save As.
Command N/A Opens a dialog that offers access to all instrument commands
(e.g. pump flow).
Fluidic Configuration N/A Opens a wizard to describe the fluidic configuration of the
system. The wizard allows the user to select a capillary kit for
a specific workflow from those capillary kits compatible with
the current hardware configuration. Alternatively, the user can
import a custom fluidic description from file.
Detach N/A Creates a new window for the ePanel that is accessible from
the PC taskbar.
Consumables Inventory Opens a floating panel that provides detailed guidance on
installation of the selected consumable. Will list top-level
<Device> device(s), that are compatible with this feature, and any
associated consumable installation guides.
Troubleshooting N/A Will either open a floating panel that offers direct access to a
specified section of the instrument user manual or an HTML
landing page with content, links, and required controls to
guide user through various troubleshooting actions.
Additionally, the following options are available for the ePanel Set:
Option Description
Autogenerated Activates automatically generated ePanel set.
Last Used Activates ePanel set contain the last manual changes.
Custom Activates a custom created ePanel set.
Manage ePanel Sets… Opens ePanel Set manager (see 3.2.1.2).
Options available when right clicking an ePanel Tab:
Option Description
Save ePanel Set As… Save customized ePanel Set.
Add ePanels… Add ePanel using the ePanel Manager.
Remove ePanel Remove currently selected ePanel.
Edit ePanel… Edit ePanel using ePanel editor (section 3.2.1.3).
Detach ePanel… Creates a new window for the ePanel that is accessible from the PC taskbar.
Manage ePanels… Opens ePanel manager (section 3.2.1.1).
Move Left Moves current ePanel left (also available by dragging the ePanel)
Move Right Moves current ePanel right (also available by dragging the ePanel)
Options available when right clicking an instrument in the navigation pane:
Option Description
Group by Controller Group instruments by instrument controller.
Add to Favorites Add instrument to favorites list.
Remove from Favorites Remove instrument from favorites list.

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3.2.1.1 ePanel Manager

The ePanel Manager manages all default and customer ePanels. The following options are available:
Option Description
Name ePanel name.
Type ePanel Type (Custom or Default).
Categories Chromatography category of the ePanel (IC, HPLC, or GC).
Module Types Module type for which the ePanel was designed.
Module ID Module ID.
Date Modified Date last updated.
Visible To Chromeleon users with access to view ePanel.
Send To Exports selected ePanel.
Import From Imports ePanel.
3.2.1.2 ePanel Set Manager

The ePanel Set Manager manages all custom ePanel sets. The following columns are available:
Option Description
Name ePanel Set name.
ePanels Lists the ePanels includes in the ePanel Set.
Associated With Select instruments to be associated with ePanel set.
Preferred On Preferred instrument for ePanel set.
3.2.1.3 ePanel Editor

ePanels are graphical representations of the instruments that they are connected to. The ePanel editor allows for creating
new ePanels or modifying existing ones. Figure 4 below shows the ePanel editor.
Figure 4: ePanel Editor
A. Toolbox – Contains a list of the controls that can be included on the ePanel (see section 3.2.1.3.1).

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B. ePanel Organizer – Displays the name of the ePanel currently being edited. If the ePanel includes sub ePanels, they
are listed below the main ePanel name (see section 3.2.1.3.2).
C. Design Surface – Displays the ePanel currently being edited.
D. Properties pane – Enables selecting characteristics of the control currently selected on the Design Surface (see
section 0).
3.2.1.3.1 Toolbox
The following controls can be displayed on an ePanel.
CM Controls:
Toolbox Control Description

Groups controls into a single box. When controls are in a group box it is possible to move or modify
them as a group.
Groups related controls into a single container. The group box provides a caption.
Organizes groups of controls on tabbed pages.
Organizes groups of controls into a container with two sections separated (horizontally or vertically) by a
bar.
Indicates the status of the device property linked to the color box. It can be linked to any instrument
property that can have only two values. The color box can display a different background and text color
for each value.
Adds the list of properties and commands for the Instrument.
Adds a Web browser for accessing information on the World Wide Web or on a local area network. It is
possible to specify the URL to display when the ePanel is opened, and to prohibit browsing.
Adds an Instrument Audit Trail. For more details see section Error! Reference source not found..
Adds a plot for displaying current signal data. Additionally, the gradient plots can be shown on this plot.
Adds a mass spectral plot.
Graphically displays a data point in a data range. It is also possible to add sliders. These are used to set
the instrument property.
Displays the current value of a property and selects a new value by either typing or selecting from a
drop-down list. If the control is linked to a property that has only discrete values, the field cannot be
edited. The value must be selected from the list.
Displays the current value of a property and selects a new value by either typing the value or selecting
from a list.
Identifies another control or when linked to a device property displays the property value.
Selects among two or more property states.
Toggles between two property states.
Executes a command, property or series of commands and properties.
Launches a definable application with optional parameters.
Groups sub ePanels into container and displays them vertically or horizontally separated.
Adds table to ePanel.
Provides embedded PDF content viewing using the installed Adobe PDF reader application.
Displays a list of the contents of a sub-folder of /InstrumentData/ for the current instrument
Third Party Controls:

Displays the Agilent ICF panel control if the Agilent Instrument Control Framework (ICF) is
installed.

Chromeleon 7

Displays the Agilent ICF configuration control if the Agilent Instrument Control Framework (ICF) is
installed.
Displays the Waters Acquity Console if the Water Acquity UPLC System Instrument Driver
Software is installed.
Displays the Trace 1300 command dialog.
Displays the TriPlus RSH status panel.
Displays the TriPlus RSH command dialog.
Displays TriPlus 100 LS status panel.
Displays TriPlus 100 LS command dialog.
Note: Each object can be moved and resized on-screen. When relevant fonts and colors can be set in the properties
pane.
3.2.1.3.2 ePanel Organizer

The ePanel Organizer gives an overview of the main ePanel and subpanels available in the main ePanel. It displays the
name of the ePanel currently being edited. If the ePanel includes sub ePanels, they are listed below the main ePanel name.
The ePanel Organizer allows the following actions:
Action Description
New Sub ePanel Creates a new (blank) sub ePanel.
Delete (Available only if a sub ePanel is selected) Deletes the selected sub ePanel.
Rename (Available only if a sub ePanel is selected) Renames the selected sub ePanel.
Save As If the main ePanel is selected, Save As saves the main ePanel and its sub ePanels to a new name. If a sub
ePanel is selected, Save As saves the sub ePanel to a new name. The sub ePanel will be available for
selection in the ePanel Manager.
Add Adds an existing ePanel as a sub ePanel.
Test Tests the ePanel in a test window.
3.2.1.3.3 Properties Pane

The Properties pane on the ePanel Editor lets you select characteristics of the control currently selected on the Design
Surface. The available properties depend on the type of the selected control. To see a brief description of a property, click its
name. The description appears at the bottom of the Properties pane. The properties pane is divided in categories, available
depending in the control:
1. Appearance (see 3.2.1.3.3.1)
2. Behavior (see 3.2.1.3.3.2)
3. Data (see 3.2.1.3.3.3)
4. Layout (see 3.2.1.3.3.4)
5. Axis / Decoration (see 3.2.1.3.3.5).
6. Current Zoom (see 3.2.1.3.3.6).
7. Default Scales (see 3.2.1.3.3.7).
8. Gradient Plot (see 3.2.1.3.3.8).
9. Tube Stripes (see 3.2.1.3.4).
10. Scale (see 3.2.1.3.5).
3.2.1.3.3.1 Appearance

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The appearance category allows changing the appearance of the selected control. The options depend on the type of
control selected. The appearance category is not available for the Web Browser control. It is possible to change:
• Color (Color, Fore Color, Back Color, Collection)
Three color palettes are available:
o The Custom palette contains the available custom colors.
o The Web palette contains the standard Web-safe colors.
o The System palette contains the standard colors provided by the operating system.
• Font (Typeface, Text Color, Text Alignment)
• Image (Not available for all controls)
3.2.1.3.3.2 Behavior
The behavior category allows setting the behavior of the selected control, for example, in this category it is possible to set
the “Show If” and “Enable If” properties and determine if dialog should be modeless.
The behavior category is not available for the Command List control.
3.2.1.3.3.3 Data
To enable the intended function of a control that you have added to an ePanel in the ePanel Editor, you must link the control
to a device property or command. This is done in the Data category.
The data category is not available for the Container, Tab Container, Split Container, Command List, Audit Trail, Web
Browser, and Signal Plot controls.
For the controls Color Box, DropDown List (only Link), Edit Field (Only Link), Gauge (Only Link), Group Box, Label, Radio
Buttons, and Switch are the following two properties available:
• Link – Links the control to an instrument property
• Caption – Adds a caption to the control. This caption can contain text and device properties.
For the Button the following options are available:
• Caption – Add a caption to the button. This caption can contain text and device properties.
• Command – Select action to perform when the button is clicked (none, run script).
• Script – Possibility to enter the command, property, or series of commands and properties to be executed when
the button is clicked.
3.2.1.3.3.4 Layout
The layout category can define the size of the selected control; it’s location on the canvas and autosize properties. This
category is available for all controls.
3.2.1.3.3.5 Axis / Decoration

The axis / decoration category allows setting all default axis and decoration parameters for the Signal Plot.
3.2.1.3.3.6 Current Zoom

The current zoom category allows setting the default axis in the zoom box in the Signal Plot.
3.2.1.3.3.7 Default Scales

The default scales allow setting the signal and time range defaults of the Signal Plot when the instrument is idle.
3.2.1.3.3.8 Gradient Plot

The Gradient Plot category allows showing the gradients used on these instruments (Eluent Composition, Flow, Eluent
Generator). The following options can be set:
• Dwell Time – Specifies dwell time in minutes
• Gradient Label – Shows labels in gradient plots
• Gradient Label Font – Defines the font for the gradient labels
• Gradient Line Style – Defines the gradient line style
• Gradient Line Width – Defines the gradient line width

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• Gradient Overlay – Indicates whether the gradient overlay is visible

• Time Marker – Defines whether the time marker is visible
3.2.1.3.4 Tube Stripes

The Tube Stripes parameter for the Signal Plot allows defining for fraction collection which channel to use for delay time
correction and whether tube stripe overlays should be visually represented on the plot.
3.2.1.3.5 Scale
The scales allow setting the intensity and mass ranges and autoscaling of the Mass Spectral Plot.

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3.2.2 Instrument Queue

The instrument queue shows a list of all sequences that are scheduled to be run on an instrument (see Figure 5 below).
Figure 5: Instrument Queue

The Queue tab has two views, selected by clicking the corresponding tab:
View Description
Current Displays the queue and the status of each sequence (see section 3.2.2.1).
Recent Displays items that have been removed from the queue within the last week (see section 3.2.2.2).
3.2.2.1 Queue – Current View

The Current view of the Queue list contains the following columns:

Startup N/A Indicates if SmartStartup runs before starting this sequence.
Name N/A Displays the sequence name and location.
Status Pending Sequence has not been started.
Running Wake-up Wake-up conditions are running.
Running Smart Startup Smart Startup conditions are running.
Running Sequence is running.
Waiting for Start Sequence with delayed start time has started, but earliest
allowable start time has not been reached.
Cancelled Queue was stopped while sequence was running (user
interaction)
Failed A module reported an error, or running sequence failed to
communicate with instrument.
Finished All injections in the sequence are completed.
Start after N/A Indicated earliest allowable start time.

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Other options on the Queue tab in the current view:

Add N/A Add a sequence to the queue.
Remove N/A Removes a sequence from the queue.
Move Up N/A Move the sequence one place up in the queue.
Move Down N/A Move the sequence one place down in the queue.
Start N/A Starts the queue.
Stop N/A Stops the queue.
Ready Check N/A Performs a ready check for the queue.
After running the queue N/A Defines action when queue is finished.
Keep instrument ready Instrument keeps running, using last conditions.
Run Smart Shutdown Instrument shuts down.
Run Smart Standby Instrument goes in standby mode.
Sequence N/A Opens the sequence properties dialog box, where auto-
report options can be configured, for the sequence currently
selected in the queue.
Emergency Instrument Method N/A Defines which Instrument Method to use when an Abort
error occurs in the queue.
3.2.2.2 Queue – Recent View

The Recent view displays items that have been removed from the queue within the last week. This view is divided with a
splitter into a grid of sequences (on top) and an injection list (read-only sequence display) below. Double-clicking a
sequence or an injection opens the Chromatography Studio.
3.2.3 Instrument Audit Trail

The audit trail records all commands executed on an instrument and all errors and warnings that occur. A separate audit trail
file is created each day. The details recorded in the audit trail are dependent on the commands that can be executed on an
Instrument. The audit trail is recorded automatically and cannot be disabled by users (including system administrators).
Figure 6 below shows some of the details commonly recorded in the audit trail.
Figure 6: Instrument Audit Trail

The instrument audit trail offers the following top-level functions:
Copy Copies selected audit trail entries to the clipboard.
Report Creates a printable HTML file of the instrument audit trail.
Filtering Provides a filtering option for each of the columns in the audit trail.
Grouping Allows the audit trail to be grouped by any of the columns available.

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Display Offers 4 options:
•All: Shows all audit trail entries
•Run Only: Shows audit trail entries related to events that occur while a
sequence is running
•Preconditions only: Shows audit trail entries related to system status prior to
an injection
•Errors and Warnings: Shows only errors and warnings
Level Offers 3 options:
Normal: Only shows audit trail entries for normal user level.
Advanced: Shows audit trail entries for normal and advanced user level.
Expert: Shows audit trail entries up to expert user level.
Next Day Shows audit trail entries for the next day.
Previous Day Shows audit trail entries for the previous day.
Search Box Allows entry of text for search purposes.
Find Next Finds the next audit trail entry that meets the search criteria.
Find Previous Finds the previous audit trail entry that meets the search criteria.
The audit trail also offers some functionality that can be accessed by right clicking on any one of the column headers:
Table Columns Allows definition of which columns should be displayed and in which order.
Fill Last Column Ensures that the last column is extended to fill an empty space.
Show Group Area Activates the grouping option.
Show Tool Strip Shows/hides the tool strip.
Finally, right clicking on any one of the audit trail entries shows in addition to the functionality described above some
additional functionality:
Select All Selects all audit trail entries.
Scale Columns to Fit Page Ensures that the audit trail columns are sized to fit the screen view.
3.3 Data Category

Selecting the data category bar changes the contents in the navigation area to a list of all Data Vaults registered on the
discovery server. The work area displays the contents of the selected object (see Figure 7 below).

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Figure 7: Data Category

The data category provides access to the following object types:
• Data Vaults (see section 4.1)
• Folders (see section 4.2)
• Sequences (see section 4.3)
• Instrument Audit Trail (see section 4.4)
• Instrument Method (see section 4.6)
• Processing Method (see section 5)
• View Settings (see section 5.4)
• Report Templates (see section 5.6)
• Electronic Reports (see section 5.8)
• Spectral Library (see section 5.9)
• MS Spectral Library (see section 5.10)
• Query (see section4.4)
• Deleted Items (see section 4.5)
• Data Audit Trail (see section 5.11)
3.3.1 Sequence Status Bar

Depending on the status of the sequence the function changes from start or stop a sequence run or resume an interrupted
sequence. Submit/Review/Approve a finished sequence (only available if electronic signatures are enabled for the
sequence). The following functions are offered for all sequences in the status bar:

Start N/A Start the current sequence
Start with Smart Startup Start the current sequence using Smart Startup to
perform instrument equilibration prior to starting
Smart Startup Run Smart Startup based on the settings in the
Instrument Method for the first injection
Add to Queue Add the sequence to the Queue without starting

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Submit Electronically submit the sequence
Resume N/A Restart the sequence at the first idle injection in the
list
Remove Remove the sequence from the Queue
View Queue Opens the Instrument ePanel
Stop N/A Stop the running sequence. The option to stop
immediately, after the current injection or after the
current sequence will be offered.
Submit N/A Apply an Electronic signature to the sequence at
the submit level
Review N/A Apply an Electronic signature to the sequence at
the review level
Remove Submit Completely remove the electronic signature
Approve N/A Apply an Electronic signature to the sequence at
the approve level
Remove Submit Completely remove the electronic signature
Remove Submit N/A Completely remove the electronic signature
Convert N/A Converts non-Chromeleon data and enables data
processing by Chromeleon.
Instrument button Open Instrument… Open a detached ePanel for the currently displayed
instrument (default action of main button)
Assign Instrument… Assign the sequence to a different instrument
Command Instrument… Opens the Command dialog and issue a command
to the instrument
3.3.2 Sequence Toolbar

The following functions are offered for all sequences in the Sequence Toolbar:

Save N/A Save any pending changes to the sequence
Studio N/A Open the currently selected injection in the Chromatography
Studio.
Print Report Print a report based on the settings in a Report Template
(default action of main button)
Injection List Print the sequence table.
Up N/A Moves to the next level directory above the current selection
in the navigation pane.
Insert Row N/A Insert one row into the Sequence table immediately above the
currently selected line/cell
3 Insert three rows into the Sequence table immediately above
the currently selected line/cell
5 Insert five rows into the Sequence table immediately above
10 Insert ten rows into the Sequence table immediately above
Fill Down N/A Copy the contents of the current cell selection to all cells
below in the same column.
Injection Locking Lock Lock the selected finished injections
Unlock Unlock the selected finished injections
Filtering N/A Display the filter bar at the top of the sequence table
Grouping N/A Display the grouping bar at the top of the sequence table

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Custom Columns Insert Result Formula Opens the Result Formula Wizard. Use the wizard to either
create a new result formula or to import a result formula from
an existing sequence.
Insert Custom Variable Opens the Custom Variables Wizard. Use the wizard to either
create a new custom injection variable or import a custom
injection variable that is already available in an existing Data
Vault or Sequence.
Edit Opens the Table Columns dialog with the properties of the
selected custom variable or result formula displayed.
Delete Removes the selected custom variable or result formula from
the table.
Text box N/A Text to find using the Find Next button
Find Next N/A Find the next occurrence of the text entered in the text box
within the sequence injection list
Find Previous Find the previous occurrence of the text entered in the text
box within the sequence injection list
3.3.3 Sequence Table Context Menu

The following context menu operations are also available:

Open Instrument Method Opens the instrument method associated with the selected
injection in the Studio window.
Injection Audit Trail Opens the injection audit trail in a new audit trail window.
Processing Method Opens the Studio window with the Data Processing category
selected. If the view setting does not contain the processing
method pane, no processing method will be visible.
All Channels Opens the Studio window with the Data Processing category
selected and all acquired channels pinned.
<Channel> Opens the Studio window with the Data Processing category
and chosen channel selected. The default channel is bolded
in the list. Selection of non-default channel will override the
default selection.
Open raw file with <Registered Software Application> Opens the injection MS raw file in the selected software
application. The function is visible only when the injection
has MS data in Xcalibur raw file format. The subfunctions
are visible only if software applications are registered under
the Operating System with the *.raw extension.
Copy N/A Copies data selected in the sequence editor to memory.
Paste N/A Pastes data in memory to the sequence. If an injection with
raw data was copied, the raw data will also be copied over.
Insert N/A Inserts an empty injection before the selected line in the
sequence.
Delete N/A Deletes the selected line(s) in the sequence editor.
Fill Down N/A Auto-populates the selected ranges of cells in the sequence
editor with the first line of the column. In the case the Name
column of the sequence is selected, a wizard to dynamically
create names will appear.
Injection Locking Lock Locks the selected finished injections.
Unlock Unlocks the selected finished injections.
Undo N/A Steps backwards through all the actions taken in the
sequence since opening.
Redo N/A Steps forwards through all actions undone.
Print… N/A Opens the Print dialogue.
Export… N/A Opens the Export dialogue for export in various formats.

Chromeleon 7

Show Data Audit Trail… N/A Opens the data audit trail in a new audit trail window.
3.3.4 Sequence Context Menu

Cut Cut selected sequence to memory.
Copy Copies selected sequence to memory.
Paste Pastes sequence in memory to specified location.
Rename Renames the selected sequence.
Delete Deletes the selected sequence.
Delete Raw Data Opens Delete Raw Data dialog providing options to delete All raw data or Selected raw data.
Print Report Defines report template and print setting for printing.
Export Opens the Export dialog. For a description of each option, refer to section 5.7.22.2.
Convert to Chromeleon Processing Converts non-Chromeleon 7 data and enables data processing by Chromeleon 7.
Read-Only Indicates if the sequence is read-only or not. Read-only sequences cannot be modified.
Send To Opens the Send to dialog for export in various formats. For a description of each option, refer to
section 5.3.9.
Show Data Audit Trail… Opens the sequence audit trail in a new audit trail window.
Properties For a description of each option, refer to section 4.3.2.

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3.4 eWorkflows Category

Selecting the eWorkflows category bar changes the contents in the navigation area to a list of all eWorkflows available in all
Data Vaults (see Figure 8 below). The work area displays details about the eWorkflow, a list of associated files (if any are
provided), and a list of all instruments capable of running the eWorkflow.
Figure 8: eWorkflow Category
The list of eWorkflows in the navigation area can be grouped and filtered. The section “More filters“can be expanded and
offers additional filtering functionality. The following options are available:

Grouping N/A Allows the list of eWorkflows to be grouped by
Data Vault
State
Tag
Type
More filters Data Vault Allows the list of eWorkflows to be filtered by Data Vault.
State Allows the list of eWorkflows to be filtered by State.
Tag Allows the list of eWorkflows to be filtered by Tag.
Type Allows the list of eWorkflows to be filtered by Type.
It is possible to startup an instrument using Smart Startup by selecting the Smart Startup option from the context menu.
3.4.1 Editing an eWorkflow

The edit screen for eWorkflows offers three tabs:
11. eWorkflow General – used to define the general settings for the eWorkflow

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12. Sequence General – used to define the general settings for the sequence that will be created from the
eWorkflow
13. Sequence Layout – used to define the injection list layout that will be provided in the sequence generated by
the eWorkflow.
3.4.1.1 eWorkflow General

The following options are available:

State N/A Allows the user to define the state of the eWorkflow. Choices
are:
•In Development
•Ready
•Approved
•Retired
General eWorkflow Type Allows the user to define a type for the eWorkflow. Choices
are:
• GC
• HPLC
• IC
• None
eWorkflow Tags Allows the user to mark the eWorkflow with Tags. Tags are
defined in the administration console.
Show Description at Launch When enabled the description of the eWorkflow is shown in
the first page of the wizard when launching the eWorkflow.
eWorkflow Description A description of the eWorkflow.
Associated Items Instruments Instruments that are capable of running the eWorkflow can
be added here. If no instrument is added, the eWorkflow will
offer all instruments in the laboratory to the user.
Methods Chromeleon methods can be added here. If one of the
following methods is not added, the user will be prompted to
supply one when running the eWorkflow:
• Instrument Method
• Processing Method
• View Settings
• Report Template
Methods can either be added directly to the eWorkflow or
added as a link.
Attachments Any file type (e.g. Microsoft Word, Adobe Acrobat) can be
added here. These can either be added directly to the
eWorkflow or added as a link.

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Figure 9: eWorkflow General Settings
3.4.1.2 Sequence General


Defaults Default Report Template Defines the default report template for the sequence that will
be created by the eWorkflow
Save only a link to the selected When checked only a link to the selected report at its current
Report Template location will be saved to the sequence. This is only available
if the report has been added as a link on the eWorkflow
General page.
Default View Setting Defines the default view setting for the sequence that will be
created by the eWorkflow
Save only a link to the selected When checked only a link to the selected view settings file at
View Settings its current location will be saved to the sequence. This is
only available if the view settings file has been added as a
link on the eWorkflow General page.
Default Channel Defines the default channel for the sequence that will be
created by the eWorkflow
Sequence General Sequence Name Provides the default sequence name. Formulas can also be
added from the following report variable categories
• Global Functions – 7.1
• General – 7.2
• eWorkflow - 7.40
If this field is left blank, users will be prompted to supply a
sequence name when running the eWorkflow
Data Vault Specifies the data vault that the sequence will be created in.
Path Provides the default sequence path. Formulas can also be
added from the following report variable categories
• Global Functions – 7.1
• General – 7.2
• eWorkflow - 7.40
If this field is left blank, users will be prompted to supply a
sequence path when running the eWorkflow

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Comment A free text entry for further information to be added to the
sequence comment. Formulas can also be added from the
following report variable categories
Global Functions – 7.1
General – 7.2
eWorkflow - 7.40
Append injection(s) if sequence Check box to allow the injections created by the eWorkflow
already exists to be appended to an existing sequence. The option to
include all/any of the following blocks is provided:
•Header Block
•Bracket Block
•Footer Block
Auto-reporting Settings Configure auto reporting… Opens the Auto reporting settings dialog (see 3.4.1.3)
Notification Settings Enable Notifications Enables configuration of notifications for sequences created
by the eWorkflow.
Send notification email when Checking the box will cause an email to be sent when the
sequence finishes normally last injection of the sequence completes to the specified
email addresses (or Chromeleon usernames)
Send notification email when Checking the box will cause an email to be sent to the
sequence is aborted by the specified email addresses (or Chromeleon usernames) if the
instrument sequence aborted by the instrument
Send notification email when Checking the box will cause an email to be sent to the
sequence is cancelled by a user specified email addresses (or Chromeleon usernames) if a
user aborts the sequence
Include the user who started the If enabled, the user who submitted the sequence to the
sequence instrument will be notified, in addition to the other recipients
specified above
Include the user who created the If enabled, the user who created the sequence will be
sequence notified, in addition to the other recipients specified above
Electronic Signature N/A Check box options to define the levels of signature required
for sequence. Options are;
•Submit
•Review
•Approve
Queue Settings Enable Smart Startup when adding Automatically run a Smart Startup procedure when a
the sequence to the queue sequence created by the eWorkflow is added to the queue.
Update Visible Views For MS Data N/A For MS data, provides an option to defer auto-processing
and updating of view panes in the Studio
Custom Variables and Formulas N/A Allows custom sequence variables and custom formulas to
be added. See 3.1.3 for more details on custom sequence
variables. See 3.1.4 for more details on custom formulas.
3.4.1.3 Auto reporting settings dialog

Auto-reporting Settings Save Electronic Report A report will be automatically created and saved for all
sequences created by the eWorkflow (can be enforced for
an instrument in Instrument Configuration Manager)
Print report A report will be automatically created and printed for all
sequences created by the eWorkflow
Export report A report will be automatically created and exported for all
sequences created by the eWorkflow
Print/Export report Determines when report will be generated. Options are:
After whole sequence (default)
After each injection

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Printer Allows a printer to be selected. This printer will become the

default printer for any report generated for any Sequence
created from this eWorkflow.
3.4.1.4 Sequence Layout

The following options are available for defining the structure of the sequence layout. Note that in this section it is possible to
define the default values for each injection (e.g. name, injection volume), the column layout (order of columns and which
columns are visible or not), and which custom injection variables are available.
Sequence Header Defines injections that must be performed at the start of the sequence. This section can be left
empty if required.
Sample Block Defines the injections that must be performed for each physical sample. For example, this can be
duplicate or triplicate injections, or unspiked and spiked injections.
Bracket Defines the injections that must be performed for each Bracket. The frequency of bracketing
injections in defined by the “Max. Samples per Bracket” option (see table below). Alternating
brackets are supported by the “No. of alternate brackets” option (see table below).
This section can be left empty if required.
Sequence Footer Defines injections that must be performed at the end of the sequence. This section can be left empty
if required.
When left empty, the default setting for position is to automatically determine the vial position when the eWorkflow is
launched. Additionally, it is possible to enter valid sampler positions such as “RA1” and numbered positions (1, 2, 3,…)
which are converted to valid sampler positions when the eWorkflow is launched.
The following options are available for defining constraints for the sequence layout:
Max. Samples per Bracket Defines the maximum number of sample blocks that can run between bracketed standards
Max. Brackets per Sequence Defines the maximum number of brackets that are allowed in the sequence.
No. of alternate Brackets Defines the number of alternate brackets. A value of zero provides 1 bracket (no alternates), a value
of 1 provides 2 brackets (1 set of alternating brackets), and so on.
Use Bracket Block after Sequence Defines if the first bracket block begins after the sequence header or not.
Header
The bottom half of the window provides a preview for the sequence.
The following options are available within the preview:

Number of Samples N/A Mimics the number of samples as entered by the user
when launching the eWorkflow.
(Instrument Selection) <No Instrument Selected> Mimics the instrument as selected by the user when
Drop list with instruments launching the eWorkflow.
Sampler start position N/A Mimics the sampler start position as entered by the user
when launching the eWorkflow.
Try Launch N/A Allows to test run the eWorkflow wizard.
3.5 Command Line Parameters

Chromeleon offers a number of command line parameters to activate Chromeleon from an external program. The following
options are available:
Function Command Line Syntax Description

Import Chromeleon data Chromeleon.exe <file path> Imports data from a single CMBX file.
backup file (.CMBX)

Chromeleon 7
Import Chromeleon Chromeleon.exe <file path> Imports an eWorkflow from a single EWBX file.
eWorkflow backup file
(.EWBX)
Import one or more Chromeleon.exe <file path> [file path2...] Imports ePanels from one or more PANX files.
Chromeleon ePanel
backup files (.PANX)
Import Chromeleon XML Chromeleon.exe <file path> Creates a sequence as defined by the imported WLEX
worklist file (.WLEX) worklist file.
Unattended Mode Unattended Optional parameter to start Chromeleon without user
interface (only available for worklist import).
Login credentials /user:<Chromeleon user> and Optional parameter to provide login credentials.
/password:<user password>
Open Chromeleon data Chromeleon.exe <URL> Opens the specified data item in the Console.
item
Open Chromeleon Studio Chromeleon.exe [/open studio] Opens the specified data item (sequence, injection and in
[/channel=channel name] <url1> [url2...] the Studio.
Show help Chromeleon.exe [/h|?|help] Shows the online help about command line parameters.

Chromeleon 7
4 Objects in the Data Category

The following objects are available in the Data Category:
• Data Vaults (see section 4.1)
• Folders (see section 4.2)
• Sequences (see section 4.3)
• Instrument Audit Trail (see section 4.4)
• View Settings (see section 5.4)
• Report Templates (see section 5.6)
• Electronic Reports (see section 5.8)
• Spectral Library (see section 5.9)
• MS Spectral Library (see section 5.10)
• Query (see section4.4)
• Deleted Items (see section 4.5)
• Data Audit Trail (see section 5.11)
This section provides details of all these objects.
4.1 Data Vaults

Data Vaults are the root directory for all Chromeleon files and directories. It is possible to connect to more than one Data
Vault. Data Vaults are based on a database container and a file system. Chromeleon supports the use of MS SQL Express,
MS SQL Server databases, and Oracle databases. Data Vaults can be located on the hard disk of a standalone PC or on a
network server and can be connected from any PC with a network link to the host server.
4.1.1 Data Vault Properties

Global policies for the data vault are defined in this section.
4.1.2 General
Read-Only Defines if a Data Vault is read-only or not.
Enable versioning and data audit trails Enables/Disables versioning (see section 6 for more details).
Enable privileged actions Enforces privileged actions for the data vault (see section 11.4.12 for more details).
4.1.3 Access Control

Add User or Group Allows specific users or groups to be allowed access to a Data Vault.
Roles Allows specific roles to be assigned to users or groups when working with objects
within the Data Vault. These roles may differ from the login role of the user
4.1.4 Downtime
Specify a period during which the Data Vault is always up Specifies that the data vault is always available.
data vault is planned to be down.
Daily downtime Specifies that the data vault is unavailable for a fixed time
period every day from x to y for a duration of z.

Chromeleon 7

Weekly downtime Specifies that the data vault is unavailable for a fixed time
period once per week on a specified day from x to y for a
duration of z.
4.1.5 Database Statistics

This tab contains a pie chart showing the used and total capacity for the database part of the Data Vault. This is only
relevant for Microsoft SQL Express based Data Vaults.
4.1.6 Raw Data Statistics

This tab contains two pie charts for the raw data part of the Data Vault. The first shows statistics for the hard drive where the
Data Vault resides and the second a breakdown of the raw data in the Data Vault.
4.2 Folders
An unlimited number of folders can be created in a Chromeleon Data Vault. The following options are available in the folder
properties:
4.2.1 General
Read-Only Defines if a folder is read-only or not
A table shows the number of each object type in the folder and any subfolders.

within the Data Vault. These roles may differ from the login role of the user
4.2.3 Raw Data Statistics

This tab contains a pie chart showing the breakdown of data contained within the folder and any subfolders.
4.3 Sequences
A sequence is a list of injections that shall be processed and/or have already been analyzed. The sequence summarizes all
injection data, for example, name, injection volume, dilution, etc.
A sequence consists of three parts; the injection list, the associated items, and the custom variables. The associated items
section stores all files associated with the sequence (e.g. instrument methods, processing methods, etc.). The custom
variables section stores all custom variables associated with the sequence.
All data entry values are checked against the allowed values. Any invalid data entries are not accepted by Chromeleon.
Figure 10 below shows a typical sequence.

Chromeleon 7
Figure 10: Typical Sequence
4.3.1 Injection List

The injection list consists of the sample list. An unlimited number of injections can be created in the list. The user can define
the order in which the table columns can be displayed as well as which columns they wish to view. The following options are
available.
Parameter Sub Parameter Description

Chromatogram N/A Shows the MiniPlot™ of the chromatogram. Different
channels can be selected.
Name N/A The injection name
Cell (only available for ASE 350) N/A The cell position
Type Unknown The injection type
Blank
Check Standard
Calibration Standard
Matrix
Spiked
Unspiked
Level N/A Defines the calibration level. Can only be used with injection
types Check Standard, Calibration Standard, Spiked, and
Unspiked.
Position N/A The injection vial position in the autosampler.
Volume N/A The injection volume of the injection.
Vial (only available for ASE 350) N/A The vial position
Instrument Method N/A The instrument method used to acquire the injection
chromatogram.

Chromeleon 7

Processing Method N/A The processing method file used to process the injection.
Extract Time (only available for ASE N/A The time stamp of the successful injection.
350)
Status Idle This is the status if the injection has not been run.
Finished All injections are automatically assigned the status Finished
after successfully running.
Interrupted If an injection stops before the end of the designated run time
it is automatically assigned the status Interrupted.
Running This is the status while the injection is running.
Inject Time N/A The date and time of the injection.
Lock Status N/A Indicates the Lock Status of the Injection
Weight N/A The weight used to calculate the content - normalized to the
basic unit - of a substance in an injection. For example, if the
calculated concentrations should always be valid for 1 mg of
an injection, the actual weight is entered; for example, 124.08
mg. Chromeleon will then divide all calculated concentrations
by 124.08.
Dilution N/A A correction value for amount calculation formulae.
IntStd N/A The Injection Variable IntStd Amount is only required for a
calibration based on a variable Internal Standard (internal or
internal/external). In this case, the column serves in the
sample list for entering the amount values of the internal
standards used for the different samples.
Replicate ID N/A Used to mark samples as Replicates.
Comment N/A A comment about the sample.
Spike Group N/A Associates unknown (unspiked) injections with spiked
injections.
Re-injections N/A Indicates the number of re-injections made by Intelligent Run
Control (IRC).
GUID N/A The globally unique identifier that was assigned to this
injection.
Autodilution Ratio N/A The sample-to-diluent ratio.
Retention Time Standard N/A Used to assign a Retention Time Standard.
Target Formula or Mass N/A Allows specification of the target detection mass, either by
entering the m/z value or by typing the chemical formula
Target Negative Adducts N/A Allows selection of one or more negatively charged MS
adducts from a dropdown list. User-defined entries are also
supported
Target Positive Adducts N/A Allows selection of one or more positively charged MS
adducts from a dropdown list. User-defined entries are also
supported
Additional columns can also be seen in the sequence table:

- Custom Injection Variables (see section 3.1.3).

Frozen Columns N/A Enter the number of columns to freeze. Frozen columns
remain in view when you scroll the injection list horizontally.
Show Result Formula Statistics N/A Displays statistical data for all result formulas included in the
Pane injection list.
Manage Order N/A Manages the order of table columns.
Move Up Moves the currently selected column up in the list.
Move Down Moves the currently selected column down in the list.
Custom Columns N/A Manages custom columns.

Chromeleon 7

Add Custom Variable… Opens the Custom Variables Wizard. Use the wizard to either
create a new variable or import a variable that is already
available for the current Data Vault.
Add Result Formula… Opens the Result Formula Wizard. Use the wizard to either
create a new result formula or to import a result formula from
an existing sequence.
Remove Removes the selected custom variable or result formula from
the table.
Column Properties N/A Shows/hides column properties
Hide Properties Collapses the column properties dialog box.
In the column properties dialog, there are several options depending on the selected column:
Format Shows the formatting properties of the column, such as the font and alignment.
Type Shows the properties of the column.
Custom Variable Shows the properties of the Custom Variable.
Result Formula Shows the properties of the Result Formula.
Statistics Shows the statistical properties of the Result Formula.
4.3.1.1 Reserved Injection Custom Variable „CM7: IntStd_Levels”

An injection custom variable with the name “CM7:IntStd_Levels” is reserved for CM internal use. If this custom variable of
type Text or List is present in the sequence, the evaluation of the Variable Internal Standard Method will use this column
instead of the IntStd column (see also 5.3.2.6 Standard Method).
4.3.2 Sequence Properties

Sequence properties are defined in this area.
4.3.2.1 General
Comment The comment for the sequence.
Instrument The instrument associated with the sequence.
Report Template Default report template to be used with sequence
View Settings Default view settings to be used with sequence
Channel Default data channel to be used with sequence
Read-Only Indicates if the sequence is read-only or not. Read-only sequences cannot be
modified.
Update Visible Views For MS Data For MS data, provides an option to defer autoprocessing and updating of view
panes in the Studio
4.3.2.2 Locks
Revoke locks Allows specific users to revoke all locks of objects that are being modified.
4.3.2.3 Signature
Signature Check box options to define the levels of signature required for sequence. Options
are;
Submit
Review
Approve

Chromeleon 7
4.3.2.4 Auto Reporting
Save Electronic Report A report will be automatically created and saved to the sequence (can be enforced
for an instrument in Instrument Configuration Manager, or inherited from the
eWorkflow definition if sequence was created from an eWorkflow)
Print report A report will be automatically created and exported for the sequence (can be
enforced for an instrument in Instrument Configuration Manager, or inherited from
the eWorkflow definition if sequence was created from an eWorkflow)
Export report A report will be automatically created and exported for the sequence (can be
enforced for an instrument in Instrument Configuration Manager, or inherited from
the eWorkflow definition if sequence was created from an eWorkflow)
Print/Export report Determines when report will be generated. Options are:
Printer Allows a printer to be selected. This printer will be the default printer for any report
generated for this Sequence.
4.3.2.5 Notifications
This tab is used to enable email notification of events related to this sequence
Function Sub function Description

Send notification email when (Checkbox) Checking the box will cause an email to be sent when the last injection of the
sequence finishes normally sequence completes
Mail recipient(s) Specifies the email addresses (or Chromeleon usernames) to whom the
notification will be sent
Send notification email when (Checkbox) Checking the box will cause an email to be sent if the sequence is aborted by
sequence is aborted by the the instrument
instrument
Send notification email when (Checkbox) Checking the box will cause an email to be sent if someone aborts the
sequence is cancelled by a sequence before it completes
user
Include the user who If enabled, the user who cancelled the sequence will be notified, in addition to
cancelled the sequence the other recipients specified above
Include the user who started If enabled, the user who submitted the sequence to the instrument will be
the sequence notified, in addition to the other recipients specified above
Include the user who created If enabled, the user who created the sequence will be notified, in addition to
the sequence the other recipients specified above
4.3.2.6 Raw Data Statistics

This tab contains a pie chart showing the breakdown of raw data contained within the sequence.
4.3.3 Injection Rack View

The injection rack view provides a graphical display of the injection vial positions for the current sequence in the assigned
instruments autosampler. The following options are available.
Copy to Clipboard Copies the current rack image to the clipboard.
Full Size Scale the rack view to full size.
Zoom in (+) Zoom into the rack view.
Zoom out (-) Zoom out of the rack view.

Chromeleon 7
In the rack view properties dialog, there are several options:

Visible Trays Show all trays Shows all configured trays for the selected autosampler if
supported.
Hide inactive tray Hides trays that are configured but do not contain any
injections (i.e. are not used) in the current sequence.
Show Overview Displays the rack overview in the top right corner of the rack
view.
Positions Displays the vial positions in the rack view. (Only visible when
zoom allows.)
Tray name Displays the tray names on the rack view.
Interactions Enable scaling Disables zooming of the rack view.
Enable rotation Disables rotation of the rack view.
4.4 Injection Query

Queries are used to search for sequences. All variables defined in section 7 can be searched for. Queries are split into two
major parts:
• Quick Search Criteria: Searches for information stored in the underlying database
• Computed Criteria: Searches for values which are calculated by Chromeleon. Searches based on these criteria
take longer to perform.
4.5 Deleted Items

Deleted Items is a special folder in each data vault in the Data category in the Chromeleon Console. It provides temporary
storage for any deleted data objects. It is possible to browse the Deleted Items contents and restore data objects that were
deleted by mistake or delete them permanently.
Any folder, sequence, or injection query can be moved to the Deleted Items folder. The following types of data can be
moved to the Deleted Items folder only when they are standalone items in a folder: instrument method, processing method,
report template, view settings, spectral library, and electronic report. If they are not standalone items, they will be
permanently deleted.
4.6 Instrument Method

The instrument method contains the instrument commands that will be executed for a sample analysis. All data entry values
are checked against the allowed values. Any invalid data entries are highlighted.
The same common commands can be used for different instruments from different vendors (e.g. Flow, Inject, Wavelength,
etc.). However, many instruments have commands that are specific to them and cannot be executed on different
instruments.
The commands available depend on the instrument that the program file is connected to. The list below shows some
commands that are applicable to the UltiMate 3000 DAD-3000(RS) detector.
4.6.1 DAD-3000(RS)
Variable Description
UV.3DFIELD.MaxWavelength The maximum wavelength of the 3D Field.
UV.3DFIELD.MinWavelength The minimum wavelength of the 3D Field.
UV.3DFIELD.BunchWidth The bunch width of the diode group.
UV.UV_VIS_1.Wavelength The wavelength setting of a single acquisition channel
UV.UV_VIS_1.Bandwidth The bandwidth setting of a single acquisition channel
UV.UV_VIS_1.RefWavelength The reference wavelength of a single acquisition channel
UV.UV_VIS_1.RefBandwidth The reference bandwidth of the 3D field

Chromeleon 7
A typical program has two different views depending on the type of instrument that is connected - a script view and a device
view. The script view (see Figure 11 below) shows a list of all the instrument commands whereas the device view (see
Figure 12 below) displays only the commands for the relevant device in a more graphically orientated away.
Figure 11: Instrument Method Script Editor View

The script editor breaks down the instrument commands into 8 blocks:
Block Description
Instrument Setup All commands in this section are executed before the instrument is made ready for
performing an injection.
Equilibration Equilibration commands.
Inject Preparation Commands in this section are used to ensure that the instrument is ready to make an
injection.
Inject Contains all commands required as part of the inject process.
Start Run Contains the commands that will be executed on receiving the inject signal.
Run Contains the timed events that must occur during a run (e.g. gradient steps).
Stop Run Contains the commands that will be executed in order to stop the run.
Post Run Contains commands required for post-run equilibration of the column; includes all
commands in the method script that are executed after Stop Run.

Chromeleon 7
Figure 12: Instrument Method Device View (WPS-3000 Autosampler)
4.6.2 Mass Spectrometers

Supported Thermo Scientific mass spectrometers use the same instrument drivers as those used by the Xcalibur
application. As such, Chromeleon allows for instrument method editing and review using the same interface in the
Instrument Method data object as seen in Figure 13 . Please consult the manuals for the respective mass spectrometers for
further information on functionality. Please consult the List of Supported Instruments for a list of supported mass
spectrometers.
Figure 13: Instrument Method Device View (Mass Spectrometer)
4.6.3 Startup / Shutdown

The instrument method also contains the instrument commands that will be executed when starting up the instrument using
Smart Startup and shutting down the instrument, or putting it in standby mode, using Smart Shutdown.

Chromeleon 7
Figure 14: Smart Startup Settings in the Instrument Method

Smart Startup and Smart Shutdown can be activated manually using the toolbar in the Instruments category, or
automatically using the Queue Settings (see section 3.2.2). Smart Startup can be manually activated from the eWorkflows
category (see section 3.4).

Chromeleon 7
5 Chromatography Studio
The chromatography studio is a user interface that provides access to all information related to a sequence. It is designed to
look like Microsoft Outlook. Figure 15 shows an example of the Chromatography Studio.
Figure 15: Overview of the Chromatography Studio

1. Category Bars, providing access to:
a. Injection List (see section 4.3).
b. Instrument Method (see section 4.6).
c. Data Processing, providing access to:
i. Processing Method (see section 5).
ii. View Settings (see section 5.4).
d. Non-Targeted MS Processing providing access to
i. Processing (See section 5.4.16).
ii. View Settings (see section 5.4)
e. Report Designer (see section 5.6).Electronic Reports (see section 5.8)
f. Spectral Library (see section 5.9).
2. Navigation Pane - Area in which you can navigate through the objects available in the selected category.
3. Work Area - The content changes according to the selected category.
4. Ribbon - Menu tool for main actions in the studio. Depending on the category or the selected pane, different
Ribbon tabs are available.
5. Studio Button - The location for commands related to general tasks (see section 5.1).
5.1 Studio Button

The Application Menu is the location for commands related to general tasks, like printing, exporting, saving, etc. The
following options are available in the Application Menu:

Chromeleon 7

New Instrument Method Creates a new Instrument Method in the current sequence.
Processing Method Creates a new Processing Method in the current sequence.
View Settings Creates new View Settings in the current sequence.
Report Template Creates a new Report Template in the current sequence.
Spectral Library Creates a new Spectral Library in the current sequence.
Open N/A Opens a sequence in a new Chromatography Studio
Add Instrument Method Adds an existing Instrument Method to the current sequence.
Processing Method Adds an existing Processing Method to the current sequence.
View Settings Adds existing View Settings to the current sequence.
Report Template Adds an existing Report Template to the current sequence.
Spectral Library Adds an existing Spectral Library to the current sequence.
Save Save Opens the save dialog with the possibility to choose data
objects to save.
Save All Immediately saves all modified objects in current sequence.
Save Sequence As Save a copy of the current sequence with a different name or
at a different location.
Save As Save a copy of the currently selected data object with a
different name at a different location.
Print Print Opens the print dialog.
Quick Print Immediately prints the currently selected document to the
default printer.
Print Preview Opens the print preview window.
Export N/A Opens the export dialog.
Convert N/A Converts non-Chromeleon data and enables data processing
by Chromeleon.
Close N/A Closes the chromatography studio.
5.2 View Settings

The View Settings stores all aspects of the data visualization of the sequence within the Chromatography Studio.
The view settings include the following settings:
• Selection of visible panes (dependent on license options).
• All visual aspects of chromatogram, calibration, spectral contour and 3D plots, such as line colors, labels to be
shown, etc.
• Selection and layout of the interactive results tables.
• The size, location and layout of the MS ‘Find in Library’ window (see section 5.4.12.9)
In addition, the pane “Presets” allows to activate a task oriented predefined pane layout with a single click. The following
presets are available:
Short name Pane selection

Results Chromatogram plot, Interactive Results Tables
Calib. & PM Chromatogram plot, Calibration plot, Processing Method
Contour & Res. Chromatogram plot, Peak properties, UV-Vis Contour plot, Interactive Results Tables
Proc. Method Chromatogram plot, Processing Method
Res & Charts Chromatogram plot, Interactive Results Tables, Interactive Charts
Calib. & Results Chromatogram plot, Calibration plot, Interactive Results Tables
Contour/3D Chromatogram plot, Peak properties, Contour plot

Chromeleon 7
PM & Results Chromatogram plot, Processing Method, Interactive Results Tables

Calibration Chromatogram plot, Peak properties, Calibration plot
UV-Vis & Res.i Chromatogram plot, Spectral plot, Interactive Results Tables
FL & Results Chromatogram plot, Fluorescence spectral plot, Interactive Results Table
MS & Results Chromatogram plot, Mass Spectrum Plot, Interactive Results Tables
MS Components MS Components plot, Mass Spectra plot, Interactive Results Table
I-t & Results Chromatogram plot, I-t plot, Interactive Results Table
Inj. Rack View Chromatogram plot, Interactive Results Tables, Injection rack view
Frac. Tray View Chromatogram plot, Interactive Results Tables, Autosampler’s fraction tray view
Atlas Chromat. Atlas orientation of Interactive Results Tables, Chromatogram plot, Processing Method
Atlas Calib. Atlas orientation of interactive Results Tables, Calibration plot, Processing Method
Atlas Spectral Atlas orientation of Spectral plot, Calibration plot, Chromatogram plot, interactive Results Tables
HRAM Quan MS Components plot, Calibration Plot, Mass Spectra plot, Processing Method, Interactive Results Table
SRM Quan MS Components plot, Calibration Plot, Interactive Charts, Processing Method, Interactive Results Table
Xcalibur Qual Chromatogram plot, Mass Spectra plot
MS Comp & PM MS Components plot, Processing Method
The “Data Processing Home” ribbon also offers cut, copy and paste operations and buttons for navigating to the
next/previous Injection, Channel and Component. All options available in each pane are listed in subsequent chapters.
5.3 Processing Method

The processing method contains all the data processing instructions (e.g. detection parameters, peak names, etc.). All the
parameters are separated out into 10 main areas, as detailed below.
Note: The layout of the processing method can be changed. The description below is based on the “Advanced” Layout.
Options can be found on different processing method tabs, depending on the selected layout. For a description of the
layouts, see section 5.3.20.
All data entry values are checked against the allowed values. Any invalid data entries are not accepted by Chromeleon.
Figure 16 below shows a typical processing method using the “Advanced” layout.

Chromeleon 7
Figure 16: A Typical Processing Method
5.3.1 Detection
The “Detection” tab holds all detection parameters for the processing method. An unlimited number of parameters can be
entered in the table. Each parameter can be activated either at the same time or at different times. Detection parameters
can be assigned to specific channels (or all channels) and to specific injection types (or all types).
Chromeleon 7 supports the Chromeleon 6 algorithm and also offers the Cobra algorithm. Details of the Chromeleon 6
algorithm are provided in the Chromeleon 6.8 functional specification. Details of the Cobra Algorithm detection parameters
are provided below.
5.3.1.1 Baseline Noise

The “Auto Range” option automatically determines a suitable time range by searching the signal for a baseline segment with
low deviation from a line.
In addition, the Start and End Times can be used to define a fixed range that is used for computing the noise in the signal for
automatic thresholds of minimum area/height detection parameters and the curvature noise for the peak and baseline
detection thresholds.
5.3.1.2 Cobra Smoothing Width

Determines the width (= time span) from which several successive data points are interpreted as peak or as noise.
5.3.1.3 Consider Void Peak

Use this parameter to hide a negative peak at the chromatogram start. This is especially useful for the negative water peak
in ion chromatography. If Consider Void Peak is set to On, peak detection is disabled for the range of the negative water
peak.
The system searches for the negative water peak in the retention time range between Consider Void Peak = On and
Consider Void Peak = Off. The negative water peak is the peak with the lowest signal at the retention time. Peak
suppression is enabled for the time between Consider Void Peak = On and the end of the negative water peak. The
chromatogram is recorded, but it is not integrated. (This corresponds to Inhibit Integration = On.) Peak detection is enabled
again only after the peak end of the negative water peak has been detected. (This corresponds to Inhibit Integration = Off.)
5.3.1.4 Baseline Point

The Baseline Point detection parameter defines a baseline point at the indicated time.
5.3.1.5 Baseline Type

Baseline Type offers various options for defining the baseline:

Chromeleon 7
Valley to Valley Enables baseline treatment from valley-to-valley, that is, from peak minimum to peak minimum, in a series of
non-resolved peaks.
Drop Perpendicular This is the default value. In case of non-resolved peaks, the baseline is not pulled up to the relative minima
(valleys). The baseline connects the start of the first with the end of the last non-resolved peak.
If one of the valleys in-between is located below the baseline, the baseline is connected with this minimum to
avoid cutting off a peak foot. The Valley-to-Valley parameter is not effective.
Lock at current level The baseline is fixed at the current signal level and is extrapolated horizontally to the right. The Valley-to-
Valley parameter will not take effect.
Lock at global minimum Chromeleon searches to the right for the next absolute minimum. The search is performed either to the end of
the chromatogram or to the next Lock Baseline. Within this interval, the baseline is locked on the found
minimum and is horizontal. The Valley-to-Valley parameter is not effective.
5.3.1.6 Detect Negative Peaks

The Detect Negative Peaks parameter enables and disables detection of negative peaks. When turned on, negative as well
as positive peaks are detected. An additional option is offered - “On Don’t Label”. This option should be used to correct the
baseline without labeling the peaks or including peaks in the peak list.
5.3.1.7 Detect Shoulder Peaks

The Detect Shoulder Peaks parameter rejects a peak if it is a shoulder.
First, the average baseline curvature is determined for the entire chromatogram. The curvature threshold value is the
product of the average baseline curvature and the threshold value.
Detected peak shoulders with a maximum curvature above this threshold value are not considered. Select the Sensitivity
detection parameter to influence the determination of the average baseline curvature. Higher sensitivity results in a smaller
average baseline curvature and thus affects peak shoulder recognition.
5.3.1.8 Fixed Baseline

The Fixed Baseline parameter defines the start and the end of a straight baseline between two data points of the
chromatogram. Start and end time of this baseline section are determined by the retention time of the corresponding Fixed
baseline detection parameter pair, i.e. Fixed Baseline = Start and Fixed Baseline = End.
5.3.1.9 Fronting Sensitivity Factor

This detection parameter is an implicit threshold for setting the peak start.
When set to Off (=0), the peak start is moved on the time axis until the slopes of the chromatogram and of the baseline
correspond in the peak start.
When set between 1 - 100 the following process is used:
First, the time for the peak start is determined as described above for Off (=0), and then the right baseline width is
determined, using the Baseline Level parameter of the Right Width peak variable or (0)). The value, which is the upper limit
for the distance between the peak retention time and the peak end, is peak.right_width multiplied by the Fronting sensitivity
factor. If this limit is exceeded, the peak start is corrected and reset accordingly.
5.3.1.10 Inhibit Integration

If the value is set to On before the first peak to inhibit, peak detection will not take place until the parameter is disabled (Off);
that is, no peaks are recognized in this area. The chromatogram is displayed on screen, but it is not integrated.

Chromeleon 7
5.3.1.11 Maximum Rider Ratio

If one or several peaks (h1 to h4) are above the Rider Threshold in a series of non-resolved peaks, Chromeleon determines
via the Maximum Rider Ratio detection parameter, whether a peak is classified as main peak or Rider.
For this, the height of the peak to classify is put in relation to the height of the greatest peak in the series (reference peak).
Figure 17: Rider Detection Parameters

As can be seen in Figure 17, not the "real" peak height of the peak to be classified is evaluated but the distance between the
peak maximum and the skimming tangent. If the ratio h/b multiplied by 100 percent produces a value larger than the one
defined as maximum rider ratio, the peak is a main peak. If the ratio h/b multiplied by 100 percent produces a value smaller
than the one defined as maximum rider ratio, the peak is a rider peak. Starting with the largest peak in the series (reference
peak), all adjacent peaks are then classified. As soon as another main peak is recognized, this peak automatically becomes
the new reference peak (b´). The maximum rider ratio is recalculated considering b´. The remaining peaks are classified
again. The process is continued until all peaks of the series are classified.
5.3.1.12 Maximum Width

The Maximum Width detection parameter defines the maximum width above which peaks are ignored during peak
detection. The peak width is measured on the baseline. For peaks that do not reach the baseline, the width is extrapolated.
5.3.1.13 Minimum Area

The Minimum Area detection parameter is used as a minimum criterion determining the area threshold below which peaks
are not integrated.
5.3.1.14 Minimum Baseline Box Width

Determines the size of the box used to search time ranges with a low curvature for the algorithm that is used to identify
peaks of the chromatogram where the baseline is measured directly (outside of a peak).
5.3.1.15 Minimum Height

The Minimum Height detection parameter is used as a minimum criterion determining the height threshold below which
peaks are not integrated.
5.3.1.16 Minimum Relative Area

Peaks are rejected if their relative area is below a given threshold.
5.3.1.17 Minimum Relative Height

Peaks are rejected if their relative height is below a given threshold.
5.3.1.18 Minimum Rider Ratio

Rejects the identification of a peak as rider if its height is below the given fraction of the height of the largest peak in the
group of neighboring unresolved peaks. See maximum rider ratio for more details.
5.3.1.19 Minimum Signal to Noise Ratio

Sets the signal-to-noise ratio for the limit of detection threshold if Minimum Area or Minimum Height are set to Auto.
5.3.1.20 Minimum Width

The Minimum Width detection parameter is used as a minimum criterion defining the minimum width below which peaks are
ignored during peak detection. Peak width is measured on the baseline. In the case of peaks not reaching the baseline, the
width is extrapolated

Chromeleon 7
5.3.1.21 Peak Group Start/End

Select the Peak Group Start and Peak Group End detection parameters to identify several successive peaks as one peak
group. A peak group that has been defined in such a way is treated as one single peak. The peak maximum of the largest
peak becomes the peak maximum of the entire group.
Two options are available – “Auto” selects the group start/end automatically, and “Fixed” uses the defined retention times for
the group start/end.
5.3.1.22 Rider Detection

This parameter defines if riders will be detected or not (On/Off). When turned On, both fronting and tailing riders are
detected. This can be further controlled by selecting either “Front Only” if only riders on the peak front should be detected,
and “Tail Only” if only riders on the peak tail should be detected.
5.3.1.23 Rider Skimming

This parameter indicates how Rider Peaks are skimmed.
• Tangential at lower peak end (default and the common skimming method): For ascending rider peaks, the peak
start, and for descending rider peaks, the peak end is defined in such a way that rider skimming is tangential to the
chromatogram.
• Tangential at both peak ends: Peak start and peak end are determined so that rider skimming is tangential at both
ends of the chromatogram.
Exponential: The chromatogram is approximated by an exponential function, so that the slope of the chromatogram and the
exponential function correspond at the peak start and the peak end of the rider peak. This option clearly distinguishes from
the two others. In most cases, Exponential maps the actual course of the curve very accurately. With this option, the rider
peak will usually receive a more realistic larger area. You can use this option only if a sufficient number of data points are
available.
5.3.1.24 Snap Baseline

By default, Cobra will use the raw data baseline as the detected baseline. In many cases this will be the correctly defined
baseline, but if this is not the case, turning off the “Snap Baseline” option will allow Cobra to detect a baseline separated
from the raw data baseline.
5.3.1.25 Tailing Sensitivity Factor

This detection parameter is an implicit threshold for setting the peak end.
When set to Off (=0), the peak end is moved on the time axis until the slopes of the chromatogram and of the baseline
correspond in the peak end.
When set between 1 - 100 and following process is used:
First, the time for the peak end is determined as described above for Off (=0), and then the right baseline width is
determined, using the Baseline Level parameter of the Right Width peak variable or peak.right_width(0)). The value, which
is the upper limit for the distance between the peak retention time and the peak end, is multiplied by the Fronting sensitivity
factor. If this limit is exceeded, the peak end is corrected and reset accordingly.
5.3.2 Component Table

The “Component Table” tab is the area where all information relating to expected peaks are entered. An unlimited number of
components can be added to the table.
Right-clicking on a cell in the table exposes the following options
Menu item Description

Copy Copies the values in the highlighted cell(s) to the Windows Clipboard
Paste Pastes the values in the Windows Clipboard to the highlighted cell(s)
Fill down When multiple cells are highlighted, copies the value in the first highlighted cell to
all of the other highlighted cell(s)
Get Current Retention Times Updates the retention times of the highlighted cell(s) based on the actual retention
times of the currently selected chromatogram and channel.
Edit Peptide Name (Appears only when the component table contains peptides). Displays an
interactive dialog for editing the peptide name. Modifications are highlighted and
may be updated by selecting from a list. When the dialog is closed, the syntax of
the edited name is validated.

Chromeleon 7
Adjust Retention Times Adjusts all of the retention times in the table by a fixed amount or a fixed
percentage
Add Confirming Peak (MS Only) Creates an additional confirming peak column in the component table.
Note that you must still manually add the masses, filters and so on.
Remove Confirming Peak (MS Only) Removes a confirming peak column from the component table. Note
that if the column contains an actual peak definition, that information will be lost.
Add Quantitation Peak (MS Only) Creates a quantitation peak column in the component table if one does
not already exist. Note that you must still manually add the masses, filters and so
on.
Remove Quantitation Peak (MS Only) Removes the quantitation peak settings for all components.
Remove Selected Peak (MS Only) Clears the settings of the quantitation or confirmation peak for the
component of the currently selected cell.
For each component, the following information can be entered:
5.3.2.1 Name
The name of the peak.
5.3.2.2 Retention Time

The expected retention time of the peak. The following options are available:
Use this component as reference component Defines if this component is a reference component for relative retention times.
Absolute Time The expected retention time of the peak in minutes.
Time distance The time distance from a user specified reference peak. Value can be negative or
positive.
Time ratio The time ratio (%) of a user specified reference peak.
Retention Time Standard Peak Area Ratio Expected retention time is dynamically determined from a valid retention time
standard using the component predefined peak area ratio.
5.3.2.3 Window
The Window parameter defines a tolerance interval within which the peak is expected. The start and end times of the
retention window result from adding the window value to and subtracting it from the retention time (retention time +/- window
value); that is, the window width is always twice as wide as the value. A peak outside this window is not identified.

Window Interpretation Absolute The window value is treated as an absolute time.
Relative The window value entered is treated as a percentage of the
expected retention time – the higher the retention time the
larger the window.
Component Match
Algorithm Retention Time The component match is only based on the expected
retention window.
Retention Time & Peak Height The component match is based on the expected retention
window and the peak height.
Retention Time & Peak Area The component match is based on the expected retention
window and the peak area.
UV Spectrum Match The component match is based on the comparison of the UV
spectrum of the peak and the UV reference spectrum of the
component.
MS Spectrum Match The component match is based on the comparison of the MS
spectrum of the peak and the MS reference spectrum of the
component.
Algorithm = Retention Time Nearest If more than 1 peak is located within the expected retention
time window, the peak nearest to the expected retention time
in the window is assigned to the component.

Chromeleon 7

First If more than 1 peak is located within the expected retention
time window, the first peak in the window is assigned to the
component.
The 2nd peak in the window If more than 1 peak is located within the expected retention
time window, the second peak in the window is assigned to
the component.
The 3rd peak in the window If more than 2 peaks are located within the expected retention
time window, the third peak in the window is assigned to the
component.
The 4th peak in the window If more than 3 peaks are located within the expected retention
time window, the fourth peak in the window is assigned to the
component.
Algorithm = Retention Time & Peak Greatest If more than 1 peak is located within the expected retention
Height time window, the greatest peak reg. the peak height in the
window is assigned to the component.
The 2nd greatest peak in the If more than 1 peak is located within the expected retention
window time window, the second greatest peak in the window is
assigned to the component.
The 3rd greatest peak in the If more than 2 peaks are located within the expected retention
window time window, the third greatest peak in the window is assigned
to the component.
The 4th greatest peak in the If more than 3 peaks are located within the expected retention
window time window, the fourth greatest peak in the window is
Algorithm = Retention Time & Peak The largest peak in the window If more than 1 peak is located within the expected retention
Area time window, the largest peak reg. the peak area in the
window is assigned to the component.
The 2nd largest peak in the window If more than 1 peak is located within the expected retention
time window, the second largest peak in the window is
The 3rd largest peak in the window If more than 2 peaks are located within the expected retention
time window, the third largest peak in the window is assigned
to the component.
The 4th largest peak in the window If more than 3 peaks are located within the expected retention
time window, the fourth largest peak in the window is assigned
to the component.
Algorithm = UV Spectrum Match Consider only peaks inside the Computes the comparison value for all peaks in the
window = Off chromatogram against the UV reference spectrum of the
component and assigns the peak with the greatest matching
value.
Consider only peaks inside the Computes the comparison value only the peaks inside the
window = On expected retention window of the component and assigns the
peak with the greatest matching value.
Algorithm = MS Spectrum Match Consider only peaks inside the Computes the comparison value for all peaks in the
window = Off chromatogram against the MS reference spectrum of the
component and assigns the peak with the greatest matching
value.
Consider only peaks inside the Computes the comparison value only the peaks inside the
window = On expected retention window of the component and assigns the
peak with the greatest matching value.
For the component match options referring to a 2nd, 3rd or 4th peak the number of peaks in the expected retention time
window has to greater or equal to the corresponding option (i.e. 2, 3 or 4). Otherwise the component is not assigned to any
peak at all.
5.3.2.4 Channel
This defines the channel that the peak details are assigned against. The choices are “All Channels” or specific channels.

Chromeleon 7
5.3.2.5 Evaluation Type

This parameter defines the peak value that is used for the quantitative analysis of the peak. The following options are
available:

Area N/A The quantitative analysis is performed using the peak area.
Height N/A The quantitative analysis is performed using the peak height.
Relative Area All Components The quantitative analysis is performed using the peak relative
area (calculated using the areas of all peaks).
Identified Components Only The quantitative analysis is performed using the peak relative
area (calculated using the areas of all identified peaks).
Exclude ISTD Components The quantitative analysis is performed using the peak relative
area (calculated using the areas of all peaks except for any
peaks defined as ISTD peaks).
Relative Height All Components The quantitative analysis is performed using the peak relative
height (calculated using the heights of all peaks).
Identified Peaks Components The quantitative analysis is performed using the peak relative
height (calculated using the heights of all identified peaks).
Exclude ISTD Components The quantitative analysis is performed using the peak relative
heights (calculated using the heights of all peaks except for
any peaks defined as ISTD peaks).
CE Area N/A Integration type for capillary electrophoresis.
CE-Area = Area / Ret. Time
5.3.2.6 Standard Method

The Standard parameter indicates the standard method to be used for calibration. The following options are available:
External The calibration curve determines the area/amount ratio.
Internal Calibration corresponds to the External Standard method. In addition, an Internal
Standard is added. The internal standard itself is calibrated as all other peaks.
When performing the integration, the calculated amounts of the remaining peaks
are corrected by the nominal/actual ratio of the internal standard. Chromeleon
recognizes any number of internal standards. Theoretically, each peak may have its
own internal standard!
Internal/External When calibrating with an internal standard, calculation is with area and amount
ratios instead of absolute areas and amounts. During integration, the area ratio is
inserted into the saved calibration function to calculate the amount ratio. The result
is the amount in relation to its reference peak. Each peak can have its own internal
standard.
Use Channel For internal and internal/external standard calibrations it is optional to specify the
channel used during calibration,
Use this component as Internal Standard (ISTD) Defines the component as an Internal Standard.
Use sample amount as reference (Variable Internal Uses the amount value defined in the sequence table rather than the amount value
Standard) defined in the Amount table.
If the custom variable with the reserved name “CM7:IntStd_Levels” is defined in the
sequence the amount value for the Internal Standard is picked from the
concentration level in the processing method given by the value of this custom
variable property of the injection.
Generally components which are used as ISTD cannot refer to another ISTD component. Yet if the custom variable
“CM7:SyringeStandard” is defined in the processing method such a reference is possible. The value of the custom variable
has to be set to an appropriate component name which is an ISTD as well. In this case the ISTD is calibrated and evaluated
against the other ISTD which is defined via the custom variable “CM7:SyringeStandard”.
5.3.2.7 Calibration Type

The Calibration Type parameter determines the Calibration Function and the Weights. The following options are available:
5.3.2.7.1 No Calibration

Chromeleon 7
When selecting “No Calibration”, the peak is not quantified.
5.3.2.7.2 Automatic Calibration

Use this option to calibrate using a calibration function. With this option enabled, you can also define the weighting and
averaging of calibration values. The following settings are possible:

Curve Fit Type Linear The calibration curve is a straight line.
Quadratic The calibration curve is a quadratic curve.
Cubic The calibration curve is a cubic curve.
Polynomial The calibration curve is a polynomial curve (maximum of 7
orders).
Power The calibration curve is a power curve.
Average Calibration Factor (AvCF) The calibration curve is a straight line through the origin. The
slope is determined by taking the average response for every
different calibration level and then average the response
factors for the different levels.
Point to Point (P-P) The calibration curve is polygon, that is, a linear interpolation
between two calibration points. If there are several replicates
of a calibration level, they are averaged before interpolation.
Base Function x Uses x as base function for polynomial curve fit.
(Available only if Polynomial is √x Uses √x as base function for polynomial curve fit.
selected under Curve Fit Type)
x2 Uses x2 as base function for polynomial curve fit.
log(x+1) Uses log(x+1) as base function for polynomial curve fit.
Weighting No Weighting Higher weighting of higher amounts.
1/Amount Nearly cancels out the weighting of higher amounts.
2
1/Amount Causes over-proportional weighting of smaller amounts.
1/Response Nearly cancels out the weighting of higher signal values. In
this case, the Y-values (dependent signal values) of the
calibration points are used as weight factors instead of the X-
values (nominal amounts).
1/Response2 Causes over-proportional weighting of smaller signal values.
In this case, the Y-values (dependent signal values) of the
calibration points are used as weight factors instead of the X-
values (nominal amounts).
1/Rel.Std.Dev. Each average level is weighted reciprocally with the
corresponding relative standard deviation.
Note: Is only available if the option “Average Calibration
Levels before Curve Fitting” is enabled.
1/Rel.Std.Dev.2 Each average level is weighted reciprocally with the
corresponding square of the relative standard deviation.
Note: Is only available if the option “Average Calibration
Levels before Curve Fitting” is enabled.
1/Log (Amount) Very strong weighting of smaller amounts in proportion to high
amounts. This function is not suitable for amount values < 1.
1/Log2 (Amount) Extremely strong weighting of smaller amounts in proportion
to high amounts. This function is not suitable for amount
values < 1.
1/Log (Response) Very strong weighting of smaller signal values in proportion to
high signal values. The Y-values (dependent signal values) of
the calibration points are used as weight factors instead of the
X-values (nominal amounts). This function is not suitable for
signal values < 1.

Chromeleon 7

2
1/Log (Response) Extremely strong weighting of smaller signal values in
proportion to high signal values. The Y-values (dependent
signal values) of the calibration points are used as weight
factors instead of the X-values (nominal amounts). This
function is not suitable for signal values < 1.
Ignore Origin (With Offset) N/A Does not force the curve through the origin.
Force Through Origin N/A Forces the curve through the origin.
Compute with Origin (Add Zero) N/A Includes the (0,0) value when calculating the curve fitting.
Average all response values of each N/A Averages all measuring points of one calibration level before
calibration level before curve fitting calculating the calibration curve from the averaged values.
(Avg)
5.3.2.7.3 Calibration of other component or peak group

This option uses the calibration curve for the selected component. The component can be selected using a drop-down box
which lists all components from the component table. A relative Response Factor can be entered.
5.3.2.7.4 Manual Calibration

This option allows the manual definition of the calibration curve. The following formula can be defined:
f(x) = C0 + C1x + C2x2 + C3x3
where C0 to C3 are user definable values
5.3.2.8 Concentration Levels
Calibration Levels The amount for the relevant calibration level (as defined in the “Level” injection field,
section 4.3.1)
Tolerance [%] The allowable deviation (Calibration Level ± Tolerance [%]) for pass or fail results
5.3.2.9 Conc. Unit

The concentration unit for the component.
5.3.2.10 Factor
The Factor is a component-specific, multiplicative factor without dimension to correct the actually measured peak area on
the basis of estimated effects.
5.3.2.11 Peak Type

The Type parameter determines the type of baseline contact and the separation of other, non-resolved peaks. The following
Autodetect The peak type is determined via an algorithm, or via detection parameters.
Rider (R) The peak is integrated as a rider.
Main (M) The peak is integrated as a main peak without baseline contact.
Baseline-Main (B-M) The peak is integrated as a main peak with right bilateral baseline contact.
Main-Baseline (M-B) The peak is integrated as a main peak with left bilateral baseline contact.
Baseline-Main-Baseline The peak is integrated as a main peak with left and right baseline contact.
Note: When Chromeleon reports the peak type, the following distinctions are made:
• In the case of rider peaks, an ascending edge is reported as “u” (u = up) and a descending edge is reported as “d”
(d = down).
• In the case of a main peak direct baseline contact on the left and/or right side is indicated by a capital B. If the
baseline below non-resolved peaks is drawn from minimum to minimum (Valley to Valley), that is from peak end to
peak end, this type of baseline contact is characterized by a small b (Figure 18).

Chromeleon 7
Figure 18: Explanation of different Peak Types
5.3.2.12 Peak Group(s)

Peaks may be grouped and then be calibrated and integrated together. Peak groups are defined in the peak group table.
Any peak group of type ‚Named Group‘ (see 5.3.4 for details) can be entered for a component. Multiple assignments are
also possible.
5.3.2.13 Comment
The comment for the peak.
5.3.2.14 Left/Right Limit

Normally, peak integration is performed automatically. It is possible to limit or extend integration on the left, right, or on both
sides with the appropriate parameters. This may be done in the component table via a left and/or a right limit.
The peak is integrated between left and right limit, that is, between:
t - LL ... t + RL
Where:
t = Retention Time
LL = Left Limit
RL = Right Limit.
5.3.2.15 Retention Index

Linear retention indexes are defined for programmed GC as well as for HPLC. On the basis of the values defined in the
component table, Chromeleon calculates the retention index for the remaining components.
5.3.2.16 Upper / Lower Confidence Probability

The confidence interval describes the range in which the "true" calibration curve will be found with a given probability. Use
the Upper and Lower Confidence Probability columns to define the component probability limits.
5.3.2.17 Previous Retention

Dialog box to define whether the retention time stored in the component table (nominal time) is used to identify a peak or
whether the detected retention time of a peak in a previous injection is used. The following settings are available:
Use recently detected retention All Injections Select if retention times of all injections are to be used.
times of
Calibration Standards Only Select if retention times of standard injections are to be used.
Set Reference Time to Last value Use the retention time of the last injection or calibration
standard.
Average of last <n> values Average the actual retention times of the last n injections for
the newly set retention time. n can be any value between 2
and 99.
Global average Use the averaged retention times of all injections actually
processed as the new set retention time.
5.3.2.18 Custom Component Variables

Custom Component variables can be created for processing methods. For details refer to section 3.1.3.
5.3.2.19 Reference UV Spectrum Settings

UV Reference spectra are used for substance identification. A UV reference spectrum can be chosen for each peak. The
reference spectra can be obtained from either a spectra library or from the apex spectrum of any peak in any sequence.

Chromeleon 7
5.3.2.19.1 Check Extrema

The parameter indicates whether the spectra search compares the number of extrema in the reference spectrum with the
ones in the peak spectrum.
5.3.2.19.2 Match Criterion

The match criterion defines the mathematical method with which two standardized spectra are compared with each other.
The signal deviation, that is, the difference between the UV spectrum and a reference spectrum at defined wavelength, is
checked (1, 2, ...) (Figure 19). Since the square of the deviations is calculated as well, the direction of the subtraction
does not matter.
Figure 19: Check Signal Deviation to determine Match Factor

The method provides a value of similarity (match) between completely different (= 0) and identical (= 1000). The following
mathematical methods are available in Chromeleon:
Least Square Forms the sum of the squared signal deviations at each wavelength and
determines the average square deviation between two spectra.
Weighted Least Square Analogous to Least Square; the squared deviations are weighted by the signal
height (for spectra extracted close to the detection limit).
Correlation Usual match criterion in statistics if a linear correlation between two curves is
presumed (similar to Least Square; usually provides the same result).
5.3.2.19.3 Relative Maximum Deviation

The Relative Maximum Deviation column allows you to enter the maximum permissible deviation of the wavelength maxima
of the reference spectra from the maximum of the current peak spectrum.
5.3.2.19.4 Spectrum Derivative

This provides the following options for spectra comparison:
Off Compares the curve shape of the spectra themselves.
st
1 Derivative Compares the curve shape of the 1st derivative of the spectra.
2nd Derivative Compares the curve shape of the 2nd derivative of the spectra.
5.3.2.19.1 Threshold
This parameter defines the threshold of the Match Factor above which two spectra may be accepted as matching.
5.3.2.19.2 Wavelength Range

The lower and upper wavelengths used for the spectra comparison.
5.3.2.20 Reference Mass Spectrum Settings

MS Reference spectra are used for substance identification. An MS reference spectrum can be chosen for each peak. The
reference spectra can be obtained from either a spectra library or from the apex spectrum of any peak in any sequence.
5.3.2.20.1 Peak Mass Spec Filter

Chromeleon 7
This parameter Indicates the scan filter used when evaluating the peak mass spectrum in the component match.
5.3.2.20.2 Ref Mass Spec Settings

These parameters define the mathematical method with which the two mass spectra are compared.
Selecting the corresponding check box will cause these parameters to be extracted from the MS Library Screening tab of
the processing method.
To use custom library search settings, the check box should be cleared. One may then specify the search parameters

Search Type Identity Three options are available:
Normal: Uses a standard pre-screen search filter. This is the default search type.
Quick: Uses a fast pre-screen search filter.
Penalize Rare Compounds: Limits the impact of rare compounds by reducing their
match factors. This option is effective only when you have selected a NIST Mass
Spectral Library (such as mainlib). It has no effect on spectra in internal NIST
libraries or other commercial libraries.
Each reference spectrum in a NIST Mass Spectral Library contains a record of other
commercial libraries containing information about the compound. A compound is
considered 'rare' if it is present in a limited number of these libraries.
Similarity Simple: Finds a large set of spectra to compare with the submitted spectrum. This
search option is generally slower than an identity search.
Hybrid: Uses a combination of the Simple and Neutral Loss search types. When
Hybrid is selected, the Search with Mol. Weight edit box under Search Options is
enabled. Enter an estimate of the submitted spectrum's molecular weight.
Neutral Loss: Compares neutral losses of the submitted spectrum with spectra in the
library data. The neutral losses in a spectrum are the mass differences between the
molecular ion and other major ions in the spectrum. For certain classes of
compounds, neutral losses can be a very characteristic spectral feature. In a Neutral
Loss search, Chromeleon identifies the molecular ion of the submitted spectrum and
includes the molecular ion in the search, along with the spectrum. Significant neutral
losses of the submitted spectrum are calculated and compared with the library data.
Hits are returned according to matches of the molecular ion and its neutral losses.
When Neutral Loss is selected, the Search with Mol. Weight edit box under Search
Options is enabled. Enter an estimate of the submitted spectrum's molecular
Search options Search with Molecular Wt When a value is supplied, searches will be restricted to library entries with the
indicated molecular weight.
Reverse Search When checked, this parameter indicates that a reverse search will be performed
instead of a standard search
Thresholds Match Factor Defines the minimum match factor below which matches will not be reported
Reverse Match Factor Defines the minimum reverse match factor below which matches will not be reported
5.3.2.21 Extracted Ion Chromatograms

The parameters used to extract ion chromatograms from mass spectrometry (MS) raw data in a sequence. Extracted ion
chromatogram (XIC) definitions for one quantitation peak and multiple confirming peaks can be created for each component
in the component table.
5.3.2.21.1 Data Range for Extracted Ion Chromatograms

When MS Detection is combined with Extracted Ion Chromatogram parameters from the Component table, in some
situations, a partial XIC is created for peak detection and integration. The extraction window is a minimum of +/- 0.5min or is
determined by the formulas:
extraction start time = retention time – display window *10
extraction end time = retention time + display window * 10
5.3.2.21.2 Display Range

The retention time range the extracted ion chromatogram for MS components will be displayed.
Use Retention Time Use the retention time assigned to the component in the component table.

Chromeleon 7
Specify Time Specify a mid-point time that is not tied to the retention time.
Use Retention Window Use the retention time window assigned to the component in the component table.
Specify Window Specify a display window that is not tied to the retention time.
5.3.2.21.3 XICs
This function opens the Update XICs window.

Update… N/A Opens the Update XICs window
5.3.2.21.3.1 Update XICs Window

This function enables automated ion ratio calculations and bulk-apply of ratio tolerances and peak coelution settings.

Target Components For all components Enables automated ion ratio calculations and/or bulk-apply of
ratio tolerances and peak coelution settings for all components.
For selected components Enables automated ion ratio calculations and/or bulk-apply of
ratio tolerances and peak coelution settings for a limited subset
of components.
<Component Names> Selection defines components where ion ratios are
automatically calculated or ratio tolerances and peak coelution
settings are applied.
Confirming Peak Ratio Calculation Calculate Ion Ratios Enables automated calculation of ion ratios
Settings
Use average of selected injections Uses user-selected injections to determine the ion ratios
Use average of all calibration Uses the average ion ratios from all calibration standards in the
standards sequence.
Use average of all calibration Uses the average ion ratios from all calibration standards of a
standards at level single level from the sequence.
<Level ID> Defines the level ID (number or name) from which the average
ion ratio is calculated from.
Ratio Tolerances and Coelution Window Type Enables bulk-apply of the Window Type parameter
Settings
<Relative / Absolute> Defines whether the Window value is interpreted as a relative
or absolute window around the target ion ratio.
Window +/- Enables bulk-apply of the Window parameter.
<Value (%)> Defines the pass/fail tolerance window around the target ion
ratio.
Ion Coelution Enables bulk-apply of the Ion Coelution parameter.
<Value (min)> Defines the maximum retention time deviation a confirmation
peak may have against the quantitation peak. This value is
always absolute.
Update ‘Include in Calibration’ to Enables bulk-apply of the ‘Include in Calibration’ option
<Option> Include / Don’t Include
Smoothing Method Enables bulk-apply of the smoothing parameters
<Method Type> Digital filter (smoothing algorithm) to apply to the data to
reduce signal noise (or select None).
Smoothing points Number of points in smoothing block
Signal Filter Settings Update filters for all ions Enables bulk-update of filters
Select best match from filters in Bulk-update of filters by selecting the best matching filter from
current injection those available in the current injection
Use this filter Bulk-update of filters to a specific filter name
<Filter> Select the acquisition filter from which the chromatogram will
be extracted or enter a custom filter.

Chromeleon 7
5.3.2.21.4 Extracted Ion Chromatogram

Shows each XIC definition on a separate tab page. There can be one XIC definition designated the MS Quantitation Peak
and multiple MS Confirming Peak definitions.

chromatogram plot preview N/A Displays a preview of the XIC plot.
Signal N/A Defines the signal parameters to use for performing the
extraction:
Type Type of extraction performed
- TIC (Total Ion Current): All ions matching the filter entered in
the Filter list will be extracted from the raw data.
- Base Peak: Base peak ions that match the filter entered in
the Filter list and/or the mass range entered in the Mass
Range(s) field will be extracted from the raw data.
- Mass Range: Ions that match the filter entered in the Filter list
and with a mass that matches the mass or mass range
entered in the XIC Mass(es) or Range(s) box will be extracted
from the raw data.
Precursor Mass Mass of the first precursor of the MS trace, if a precursor is
defined by the filter.
XIC Mass(es) or Range(s) Mass or mass range to limit the data extracted to ions from the
selected filter that match the masses entered.
Filter Select the acquisition filter from which the chromatogram will
be extracted or enter a custom filter.
Smoothing Digital filter (smoothing algorithm) to apply to the data to
reduce signal noise (or select None).
Calibration Include in Calibration (Confirming peaks only) When selected, the response of this
peak is added to that of the quantitation peak for purposes of
calibration
Ratio N/A Enables options to compare the confirming ion's response as a
ratio of the quantitation ion's response.
Target Ratio Target ratio of the confirming ion's response to the quantitation
ion's response.
Window type Type of calculation (Absolute or Relative) used to determine a
range of ratios in which the target ratio is considered
acceptable.
Window +/- Ion ratio percent (%) to be added before and after the target
ratio.
Ion Coelution Maximum acceptable difference in retention time (in min)
between a confirming peak and a quantitation peak.
Use default MS Detection settings N/A Select this check box to use the default settings defined on the
MS Detection Settings page of the processing method.
Clear this check box to enter custom MS detection settings.
For a description of each option, refer to section 5.3.9.
Spectral plot preview N/A Shows the spectrum for the selected filter that is nearest the
extraction time and is within the extraction window.
5.3.2.22 Mol. Mass

The molecular mass of the component. It is, only used for reporting purposes.
5.3.2.23 CAS
Chemical Abstracts Service (CAS) registry number of the component, only used for reporting purposes.
5.3.2.24 Chem. Formula

Chemical structure of the component represented by text (letters and numbers), only used for reporting purposes.

Chromeleon 7
5.3.2.25 RTS Ratio Standard

The tolerance (%) that defines a range of acceptable peak area ratio values. Used to confirm a match with a component
when using a Retention Time Standard Processing Method.
5.3.3 Calibration
The “Calibration” tab is the area that shows all the global calibration settings and the list of calibration standards that are
used to quantify the peaks in the currently active chromatogram. In this tab it is possible to disable/enable the calibration
points for specific peaks/channels. Additional options available are:

Mode Fixed The calibration standards from a selected sequence are used
for calibration. The other sequence is copied to the calibration
table in the processing method. You can update the calibration
any time, for example, after the other sequence has been
updated.
Total Calibration is performed using all valid calibration standard
samples of the sequence.
Additional For calibrating a sample, all calibration standard injections that
are listed before this sample in the sample list are used.
Group The calibration of a sample series from the sample list (for
example, samples 3 to 50) is performed based on the
calibrations standards listed directly before this series; for
example, no. 1 and 2. If this sample list includes further
standards, as for instance, no. 51 and 52, the following
samples, for example, 53 to 100, will be evaluated based on
these. The standard samples in lines 1 and 2 will no longer be
considered.
Bracketed Samples are evaluated based on all calibration standards
immediately surrounding. In case of a list containing two
samples, two calibration standards, two samples, two
calibration standards and so on, samples 1 and 2, located at
positions 3 and 4, are evaluated with standards 1, 2, 3, and 4,
located at positions 1, 2, 5, and 6. Samples 3 and 4 are
evaluated using the standards 3, 4, 5, and 6, located at
positions 5, 6, 9, and 10.
Standard Addition Calibration is performed using spiked and unspiked injections.
Curve Fitting Normal Selects normal dependent and independent variables for
calibration i.e. x-axis = amount, y-axis = measured value.
Inverted Selects inverted dependent and independent variables for
calibration i.e. x-axis = measured value, y-axis = amount.
Dual-Column Separate Calibration N/A When this function is enabled it is possible to use only the
standards for the active column in tandem mode.
Concentration Level Tolerances N/A When this function is enabled, it is possible to define %
tolerances on a level-by-level and component-by-component
basis and allows for visualization of results on the calibration
plot.
Amount Ratio for Variable Internal Selecting this check box when performing variable internal
Standard standard calibration will plot the response ratio against the
amount ratio on the calibration curve and adjust the response
factors accordingly.
This check box is selected by default for new processing
methods created using Chromeleon 7.2.6 and later versions. It
is unselected by default for processing methods created using
a previous version of Chromeleon.
Origin of Standards for Fixed N/A Allows the user to select an external sequence for calibration.
Calibration On selection, all standards in the external sequence are copied
into the current sequence.
5.3.4 Peak Group Table

This section is used to define the naming and quantitation options for peak groups. For every peak group record the
following options are available:

Chromeleon 7
Name The name of the peak group.
Group Type Two peak group types are available:
Timed Group: Defines a peak group which spans over a certain time interval in the chromatogram
allowing to incorporate also unidentified peaks in a peak group. The time interval is defined by the
Start/End Time properties (see below).
Named Group: So-called named peak groups can be selected in the component table. Every
component can be assigned to 1 or more named peak groups.
Start Time The start time for the peak groups of type ‘Timed Group’.
End Time The end time for the peak groups of type ‘Timed Group’.
Channel The assigned channel for the peak group. Similar to components peak groups can be assigned to ‘All
Channels’ or to single ones.
Group Evaluation Three evaluation types are available:
None: there is no group evaluation at all. This type e.g. can be used to combine multiple disjunct
timed groups together to a single name group.
Reporting: results of peak groups (e.g. group area) can be reported in a dedicated report table.
Calibration: this type also contains the reporting capabilities but beyond that such a peak group can
be also calibrated. A component record can refer to such a peak group when setting the calibration
type to ‘Calibration of other component or peak group’ (see 5.3.2.7.3 Calibration of other component
or peak group).
Evaluation Type Evaluation Type for quantitating the peak group. Same as for the Evaluation Type in the component
table (see section 5.3.2.5 for details).
Standard Method Similar to the standard method field of the component table a peak group has its own standard
method. Possible values are External and Internal referring to an associated ISTD component.
A peak group can never be specified as an ISTD itself.
Calibration Type Calibration Type for quantitating the peak group. Same as for the Calibration Type in the component
table (see section 5.3.2.7 for more details). This property is only available for peak groups with group
evaluation ‘Calibration’.
Peak Group(s) Timed peak groups can be assigned to named groups thus extending the scope of named groups.
For named peak groups such an assignment is not available.
Include Identified Peaks Via this property the identified peaks in the time window (Start/End Time) can be included in
corresponding timed group.
Factor Multiplicative factor without dimension to correct the actually measured peak area on the basis of
estimated effects.
Comment Arbitrary user comment
Calibration Level(s) Similar to the calibration levels of the component table the calibration level is used to enter to
reference amount of a peak group. If this value is empty and the group type is ‚Named Group’ the
calibration level values of all component records which are member of this peak group are summed
up to give the reference amount of such a named peak group.
Analogue to the component table custom variables can be added to the peak group table as well.
5.3.5 Chromatogram Subtraction

This tab defines any baseline subtractions performed.
No Subtraction Blank run subtraction is not performed.
Subtract recent Blank Run injection in corresponding The blank run in the corresponding sequence is subtracted point by point from all
sequence samples.
Subtract a fixed injection Allows the user to select a blank run or other chromatogram from any sequence.
This chromatogram is subtracted point by point from all samples.
5.3.6 UV Spectral Library Screening

To identify substances, UV spectra can be compared to library spectra. The spectra search can be performed via the
Spectra Library Screening tab of the Processing Method. The following options are available:

Chromeleon 7

Spectral libraries to be searched in N/A The spectral libraries to be searched in.
Compare Conditions Match Criterion As per 5.3.2.19.2.
Hit Threshold As per 5.3.2.19.1.
Use Spectrum Derivative As per 5.3.2.19.4.
Wavelength Range As per 5.3.2.19.1.
Library Spectral Filter N/A Defines additional conditions for spectra matches.
Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
with variable values that match all of the criteria specified in
the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injections
with variable values that match any of the criteria specified in
the rules that are assigned the OR logical operator.
Variable Selects a hit spectrum variable from the list.
Comparison operator Select the operator to be used for comparing variable values:
= (is equal to)
<> (is not equal to)
< (is less than)
<= (is less than or equal to)
> (is greater than)
>= (is greater than or equal to)
is between
is not between
is during previous
is not during previous
is like (use with wildcards) (for Quick Search only)
is not like (use with wildcards) (for Quick Search only)
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Value Select the compare value.
5.3.6.1 UV Spectra
For a better comparability of UV spectra, it is useful to subtract the baseline spectrum (of the solvent). Chromeleon performs
this automatically using the following algorithm:
• The baseline spectra are determined for both peak ends. At both peak ends, several UV spectra can be averaged
over a specified range.
• The baseline peak spectrum (usually at the peak maximum) is determined via linear interpolation of these two
baseline spectra and subtracted from the single spectrum (usually of the peak maximum).
Peak Spectrum Bunch Number of single spectra to be bunched to form the spectrum at the peak
maximum.
No Baseline Correction. Baseline correction is disabled.
Peak Dependent Correction Allows automatic background subtraction for each peak. In the edit fields under left
region bunch and right region bunch the number of spectra to be used for forming
the two background spectra can be entered.
Fixed Correction Defines two fixed ranges for background subtraction for the entire chromatogram.

Chromeleon 7
This section also contains default settings for UV Spectra Comparison:
Match Criterion As per 5.3.2.19.2.
Use Spectrum Derivative As per 5.3.2.19.4.
Restrict Wavelength Range As per 5.3.2.19.1.
Peak Purity Threshold A limit for the signal height above which spectra comparison is performed for the
UV spectra.
5.3.7 SST/IRC
As defined in cooperation with EURACHEM, System Suitability Checking (SSC) or System Suitability Test (SST) is "a series
of tests to check the performance of a measuring process" [P. Bedson and M. Sargent, Accred. Qual. Assur. (1996) 1, 265-
274]. The aim and objective of System Suitability Testing is to ensure the performance of the operating system and the
system. To this has been added Intelligent Run Control (IRC) which enables the user to perform further actions based on
the results of the System Suitability Test Case. Different actions can be set for a passed and a failed test case. It is also
possible to create an Unconditional Test Case whereby the desired actions are performed for every injection which satisfies
an injection condition. When creating a new test case, it is now possible to copy an existing test case. It is also possible to
associate more than one IRC action to a given test case.
5.3.7.1 Test Cases

The following templates are available when creating a new system suitability test case.
Custom Test Blank test case with no conditions defined.
Autodilution (Large/Small Loop) Determines peak amount for a particular component based on the null and
maximum amounts defined by the calibration levels and is designed to work with a
Large/Small Loop Autodilution setup.
Autodilution (Partial Loop) Determines peak amount for a particular component based on the null and
Partial Loop Autodilution setup.
Autodilution (Vial to Vial) Determines peak amount for a particular component based on the null and
Vial to Vial Autodilution setup.
Autodilution (Amount Limits) Determines peak amount for a particular component to null and maximum amounts
defined in calibration levels.
Peak Amount Limits Compares the calculated peak amount for a particular component to the minimum
and maximum amounts defined in calibration levels.
Peak Asymmetry Determines the peak asymmetry and ensures it is less than or equal to a specified
value.
Peak Width (5%) Determines the peak width at 5% of the peak height and ensures it is less than or
equal to a specified value.
Peak Width (baseline) Determines the peak width at baseline level and ensures it is less than or equal to
a specified value.
Resolution (EP) Using EP formula, resolution is calculated against the next peak in the
chromatogram and evaluated so that it is greater than or equal to a specified value.
Resolution (USP) Using USP formula, resolution is calculated against the next peak in the
chromatogram and evaluated so that it is greater than or equal to a specified value.
Retention Time Checks that the detected retention time of a peak is greater than or equal to a
specified value.
RSD of Peak Areas Determines relative standard deviation of the peak area for between 2 and 6
injections and evaluates that the result is less than a specified value.
RSD of Peak Retention Times Determines relative standard deviation of the peak retention time for between 2
and 6 injections and evaluates that the result is less than a specified value.

Chromeleon 7
RSD of Peak Heights Determines relative standard deviation of the peak height for between 2 and 6
injections and evaluates that the result is less than a specified value.
Signal Noise Checks that the chromatogram noise across the time range used for peak
detection is less than or equal to a specified value.
Signal / Noise Ratio Checks that the signal to noise ratio is greater than or equal to a specified value.
Theoretical Plates (EP) Using EP formula, theoretical plates are evaluated so that the result is greater than
or equal to a specified value.
Theoretical Plates (JP) Using JP formula, theoretical plates are evaluated so that the result is greater than
or equal to a specified value.
Theoretical Plates (USP) Using USP formula, theoretical plates are evaluated so that the result is greater
than or equal to a specified value.
5.3.7.2 SST/IRC Conditions

This tab page lists test cases and their defined test conditions.

Name N/A Gives a description of the test case.
Statistics None No statistical evaluation is performed.
Average Average value of the aggregated injections.
Maximum Maximum value of the aggregated injections.
Minimum Minimum value of the aggregated injections.
Range Result range of the aggregated injections.
Relative Range Relative result range of the aggregated injections.
Relative Standard Deviation Relative standard deviation of the aggregated injections.
Standard Deviation Standard deviation of the aggregated injections.
Statistics Condition N/A Defines which injection results will be included in the statistical
calculations.
Include at least n and at most n Defines the minimum and maximum number of injections to
injections (incl. current injection) use for the statistics calculations.
Only include injections with The statistics calculation will only be applied to injections that
fulfill the specified rules. Any variable from the “Injection” list
(see sections 0) can be selected. The user enters a value and
then selects one of the following restriction options: -
=
<>
>
<
>=
<=
contains
doesn’t contain
starts with
doesn’t start with
ends with
doesn’t end with
The compare value is typed or selected from the list. More
than one value may be required, depending on the selected
comparison operator.
Evaluation Formula N/A The formula can be based on variables from all the areas
detailed in section 7.
Operator = Restricts the data points shown based on comparing the
selected variable with a user-defined value and using the
<> following logical arguments:
<= Is equal to

Chromeleon 7

< Is not equal to
Is smaller than or equal to
>=
Is smaller than
> Is larger than or equal to
contains Is larger than
Contains
doesn’t contain
Does not contain
starts with Starts with
doesn’t start with Does not start with
ends with Ends with
Does not end with
doesn’t end with
Is between
between Is not between
not between
Reference Value 1 N/A The Reference Value variable returns the reference values
that are compared against the evaluation value. The formula
can be based on variables from all the areas detailed in
section 7.
Reference Value 2 N/A Second Reference Value available when operator is set to
between or not between.
Channel Default channel Sequence default channel (if one is selected).
Channel name List of available channels acquired during sample run.
Peak All components Applies the test for all identified peaks (components).
Component name Applies the test to the specified peak (component).
Detected peak number Applies the test to the peak with the specified peak number.
Detected peak with The peak with the lowest/highest value for the variable
selected for this option. Variables can be selected from the
“Peak Results”, “Peak Calibration”, and “Peak Purity and
Identification” variable groups (see sections 7.9, 7.11, 7.12).
N.A. Failed Details the result reported if the test cannot be evaluated. Can
be set to either “Passed” or “Failed”.
Passed
Fail Action Continue Details the actions that CHROMELEON must take if the test
fails. Can be set to either “None” or “Abort queue”.
Abort queue
Injection Condition Apply to all injections Applies the test for all types of injections.
Injection type Applies test for the selected injection type only (see section
4.3.1).
Injection property The test will be run only for injections that fulfill the specified
rules. Any variable from the “Injection” or “Sequence” lists (see
sections 0, 7.3) can be selected. The user enters a value and
then selects one of the following restriction options: -
=
<>
>
<
>=
<=
contains
doesn’t contain
starts with
doesn’t start with
ends with
doesn’t end with
The compare value is typed or selected from the list. More
than one value may be required, depending on the selected
comparison operator.

Chromeleon 7

Custom condition Applies the test to the injections corresponding to the freely
selectable injection condition.
Result N/A Result of the system suitability test case.
SST Message N/A Additional information about the performed the SST test case.
Pass Action Abort Details the actions that CHROMELEON must take if the test
passes. This can be set to Abort, Arithmetic Combination,
Arithmetic Combination Autodilution, Copy Channel, Derivative, Extract from 3D
Autodilution Channel, Extract MS Channel(s), Extract Opt. Int. Channel,
Insert Injection, Pause, Power Law, Re-inject or Smooth
Copy Channel Channel.
Derivative
In the case of an unconditional test case, the pass actions
Extract from 3D Channel detail the actions that CHROMELEON must take for every
injection which meets the injection condition.
Extract MS Channel(s)
Extract Opt. Int. Channel
Insert Injection
Pause
Power Law
Re-inject
Smooth Channel
Fail Action Abort Details the actions that CHROMELEON must take if the test
fails. This can be set to Abort, Arithmetic Combination,
Arithmetic Combination Autodilution, Copy Channel, Derivative, Extract from 3D
Autodilution Channel, Extract MS Channel(s), Extract Opt. Int. Channel,
Insert Injection, Pause, Power Law, Re-inject or Smooth
Copy Channel Channel.
Derivative
Extract from 3D Channel
Extract MS Channel(s)
Extract Opt. Int. Channel
Insert Injection
Power Law
Re-inject
Smooth Channel
Abort N/A Aborts the queue
Arithmetic Combination Channel A Defines the channel from the current injection to be used in
the combination.
Factor A Determines the multiplying factor to be applied to Channel A
before combining it with Channel B.
Channel B Defines the second channel for the combination.
Factor B Determines the multiplying factor to be applied to Channel B
before combining it with Channel A.
Operation Defines the arithmetic operation to be performed on the two
channels selected. The following options are available: +
(addition), - (subtraction), * (multiplication) and / (division).
Result channel Defines the name for the result channel
Autodilution Processing Method Assigns processing method to be used.
Instrument Method Assigns instrument method to be used.
Injection Volume Defines injection volume in microliters (µl).
Weight Defines weight correction variable.
Internal Standard Amount Defines quantity of internal standard added to the analyzed
sample.

Chromeleon 7

Dilution Factor Defines the value of dilution, where a value of 1 indicates that
there was no dilution.
Comment Allows a user-defined comment to be added.
Replicate ID Defines the replicate ID.
Type Defines the injection type.
Concentration Level Defines the concentration level.
Position Defines the position on the autosampler rack from which the
sample is to be injected.
Spike Group Defines a spike group for the injection. This allows unspiked
(unknown) injections to be associated with spiked injections.
Max. no of re-injections Defines maximum number of re-injections to be carried out.
Copy Channel Original channel Defines the channel from the current injection to be copied.
Derivative Original channel Defines the channel from the current injection to be
derivatized.
Derivative The derivative level is selected here. This can be set to first or
second
Extract from 3D Channel Source 3D field Defines the 3D field to be extracted.
Wavelength Defines the wavelength at which the extraction should take
place
Use interpolation Defines whether the resulting chromatogram retention times
should be interpolated to 1 second intervals.
Bandwidth Defines the bandwidth for the extraction.
Extract MS Channel(s) Trace Specify the chromatogram trace type to be extracted:
TIC (Total Ion Current)—all ions matching the filter entered in
Base Peak—base peak ions that match the filter entered in
Mass Range—ions that match the filter entered in the Filter list
and with a mass that matches the mass or mass range
entered in the Mass range(s) box will be extracted from the
raw data.
Precursor Defines the precursor ion mass to reduce the list of filters in
the Filter list to only those filters with a matching precursor ion
mass.
Mass ranges Defines the mass, mass range, or a set of mass ranges to be
extracted
Filter Specifies the acquisition filter from which the chromatogram
will be extracted
Channel Name Defines the label that will be used to identify this extracted ion
chromatogram in the channels list
Smoothing Specifies the type of smoothing to be performed on the
chromatogram data when it is extracted.
Pts. Defines the number of data points for smoothing.
Extract Opt. Int. Channel Source 3D field Defines the 3D field to be integrated.
Original channel Defines the original channel
Bandwidth The bandwidth for the integration is specified here
Insert Injection Source injection The injection to be inserted is selected here.
Max. no of insertions The maximum number of times to perform the insertion is
determined here. Range is from 1 to 9999.

Chromeleon 7

Power Law Original channel Defines the channel to which the power factor should be
applied
Power factor The power factor to be applied is selected here. Range is from
1.0 to 2.0.
Re-inject Current injection Allows the user to re-inject the current injection
Completed injections Allows the user to restart the sequence
From most recent Allows the user to select anywhere else in the sequence from
which to re-inject
Max. no of re-injections The maximum number of times to perform the re-injection is
determined here. Range is from 1 to 9999.
Smooth Channel Original channel Defines the channel to be smoothed
Filter type Defines the smoothing algorithm to be used. Four options are
available: Savitzky-Golay, Moving Average, Olympic and
Gaussian.
Filter size Defines the number of data points used to generate each
output data point in the smoothed chromatogram. This is an
odd number between 3 and 999.
If an action fails to execute Continue to the next action Determines what CHROMELEON should do if an action from
a test case cannot be executed.
Continue to the next test case
Continue to the next injection
Pause the queue
Abort the queue
Rounding N/A The values for the evaluation result and reference value are
rounded to the specified decimal places.
5.3.8 Advanced Settings

On this tab it is possible to specify some more advanced settings.

Comment N/A Gives a description of the processing method.
Amount Interpretation: Reference Use inject volume of first standard Uses the injection volume of the first standard as basis for all
Inject Volume amount calculations.
Fixed Uses a fixed injection volume, entered in the box on the right,
as basis for all amount calculations.
Retention Time Settings Use absolute greatest signal value Uses the retention time of the absolute greatest signal value.
Use relative greatest signal value Uses the retention time of the signal value that is relatively the
over the baseline greatest value over the baseline.
Dead/Delay Time(s) Dead Time Specifies the dead time of the method.
2nd Detector Specifies the delay time of the second detector.
3rd Detector Specifies the delay time of the third detector.
Matrix Correction Enable Matrix Correction Enables matrix correction, where peak areas (or heights) from
matrix blank injections are subtracted from the other injections
in the sequence.
5.3.9 Composite Scoring

This tab allows users to set up pass / indeterminate / fail levels, select specific criteria to test components against, and set
tolerances for certain criteria.

Chromeleon 7

Pass score if at least <number> N/A Minimum number of passing criteria required for a component
criteria passed to pass scoring. If number of criteria passed are greater than
the failure requirement and less than the pass requirement,
the score will be indeterminate.
Fail score if less than <number> N/A Maximum number of failing criteria required for a component
criteria passed to fail scoring. If number of criteria passed are greater than
the failure requirement and less than the pass requirement,
the score will be indeterminate.
Amount based peak identity (Checkbox) Enables scoring criteria based on calibrated amounts between
verification user-selected channels with user-defined tolerances.
Disabled by default.
Reference Channel Defines the reference channel for amount-based component
verification. Confirmation channel to reference channel ratio
approaches 100% as calculated amounts for each channel
approach unity.
Confirmation Channel Defines the confirmation channel for amount-based
component verification. Confirmation channel to reference
channel ratio approaches 100% as calculated amounts for
each channel approach unity.
Tolerance Maximum deviation allowed between reference and
confirmation channel for a passing result. Allowable range of
0.1 to 50%.
Confirming ion ratio passed (Checkbox) Enables scoring based on confirmation ion ratio and ion
coelution criteria as defined by the specifications in 5.3.2.21.2.
Enabled by default.
Isotopic dot product (Checkbox) Enables isotopic dot product scoring for specific imported data
types and raw data combinations. Disabled by default
(Number) Defines minimum pass criteria for imported data types and
raw data combinations.
Mass accuracy (Checkbox) Enables mass accuracy scoring for specific imported data
types and raw data combinations. (Disabled by default)
(Number) Defines maximum deviation value from target mass of
component peaks.
(Dropdown) Defines deviation units for mass accuracy scoring.
Peak apex alignment (Checkbox) Enables peak apex alignment based on peak grouping for
specific imported data types and raw data combinations.
Disabled by default
(Number) Defines allowable peak apex retention time standard deviation
across component peaks in a group.
5.3.10 MS Detection
This “MS Detection” tab holds all MS component detection parameters for the processing method. A set of parameters can
be applied globally for all components, individually for select components, or individually for all components.
Chromeleon 7.2 supports 4 algorithms: Chromeleon 6, Cobra, Genesis, and ICIS. Details of the Chromeleon 6 algorithm
are provided in the Chromeleon 6.8 functional specification. Details of the Cobra algorithm detection parameters are
provided in section 5.3.1. Details of the Genesis and ICIS algorithms are provided in the following subsections.

Extracted Ion Chromatogram MS Default Detection Settings Displays editable global MS component detection parameters
(Component Name) Displays editable component-specific MS component
detection parameters. If Use MS default detection settings is
enabled, the global MS component detection parameters will
be displayed
Use MS default detection settings (Checkbox) Displays global MS component detection parameters when
selected. Enabled only when Extracted Ion Chromatogram
sub-parameter selected is (Component Name)

Chromeleon 7

Detection Algorithm Chromeleon 6 Chromeleon 6 detection algorithm. See Chromeleon 6.8
functional specifications for details
Cobra Cobra detection algorithm. See section 5.3.1for details
Genesis Genesis detection algorithm. See section 5.3.10.1 for details
ICIS ICIS detection algorithm. See section 5.3.10.3 for details
Run Cobra Wizard … (None) Starts the Cobra algorithm peak detection wizard. See
section 5.3.13 for details
5.3.10.1 Data Range for MS Components

When MS Detection is combined with Extracted Ion Chromatogram parameters from the Component table, in some
situations, a partial XIC is created for peak detection and integration. The extraction window is a minimum of +/- 0.5min or is
determined by the formulas:
extraction start time = retention time – display window *10
extraction end time = retention time + display window * 10
5.3.10.2 Genesis Algorithm

This algorithm is recommended for processing data with noisy baselines such as full scan MS data acquisition

S/N threshold (None) Changes the threshold for detecting peak edges
Enable valley detection (Checkbox) Enabling this option allows the algorithm to drop a vertical line
from the local minima of the valley between unresolved peaks
to the baseline. The intersection of the vertical line and the
baseline defines the end of the first peak and the beginning of
the second peak.
Expected width (sec) (None) Enabled only if the Enable valley detection parameter is
enabled. This value controls the minimum width that a peak is
expected to have if valley detection is selected.
Any valley points nearer than the expected width/2 to the top
of the peak are ignored. If a valley point is found outside the
expected peak width, the algorithm terminates the peak at that
point. The algorithm always terminates a peak when the
signal reaches the baseline, independent of the value set for
the expected peak width.
Constrain peak width (Checkbox) Enabling this option allows the algorithm to limit the peak
width of a component during peak integration.
Peak height (%) (None) Determines the peak height at which the peak width is tested
Tailing factor (None) Enabled only if the Constrain peak width parameter is
enabled. This value determines how the algorithm integrates
the tail of a peak.
This factor is the maximum ratio of the trailing edge to the
leading side of a constrained peak.
Peak S/N cutoff (None) Determines the signal-to-noise level the algorithm defines as
the peak start and end points.
Rise percentage (%) (None) Defines the percent value that a chromatogram can rise
above the baseline after passing through a minimum. When
the chromatogram exceeds this value, the algorithm applies a
valley detection peak integration criterion.
Valley depth (None) Determines the signal-to-noise ratio used for valley detection
Calculate noise as RMS Calculates noise as RMS
Peak to Peak Calculates noise as peak-to-peak
Baseline noise tolerance (None) Defines how the baseline is drawn in the noise data. The
higher the baseline noise tolerance value, the higher the
baseline is drawn through the noise data
Min scans in baseline (None) Defines the number of scans the algorithm uses to determine
the baseline

Chromeleon 7

Baseline noise rejection factor (None) Defines the width of the RMS noise band above and below
the peak detection baseline. This factor is applied to the raw
RMS noise values to raise the effective RMS noise used by
the algorithm. The algorithm responds by assigning the left
and right peak boundaries above the noise and closer to the
peak apex value in minutes. This action effectively raises the
peak integration baseline above the RMS noise level.
5.3.10.3 ICIS Algorithm

This algorithm is recommended for data with low noise or abstracted data such as SIM and SRM data acquisition as well as
XIC data

Area noise factor (None) Determines the noise level multiplier used to determine the
peak edge after the location of the possible peak
Peak noise factor (None) Determines the noise level used to determine the potential
peak signal threshold
Baseline window (None) Determines the number of scans to review, looking for a local
minima, to determine the baseline
Constrain peak width (Checkbox) Enabling this option allows the algorithm to limit the peak
width of a component during peak integration.
Peak height (%) (None) Determines the peak height at which the peak width is tested
Tailing factor (None) Enabled only if the Constrain peak width parameter is
enabled. This value determines how the algorithm integrates
the tail of a peak.
This factor is the maximum ratio of the trailing edge to the
leading side of a constrained peak.
Noise method Incos Forces algorithm to use a single pass to determine the noise
level
Repetitive Forces algorithm to use multiple passes to determine the
noise level. Incurs a performance hit compared to Incos
Min peak width (None) Determines the minimum number of data points required for a
peak
Multiplet resolution (None) Determines the minimum number of scans required between
apexes of two potential peaks to be considered resolved
Area tail extension (None) Determines the number of scans past the peak end to use in
averaging the intensity
Area scan window (None) Determines the number of scans on each side of the peak
apex to include in the area integer
RMS (Checkbox) Enabling this option allows the algorithm to calculate noise as
RMS. When disabled, the algorithm uses peak-to-peak noise
calculation
5.3.11 MS Settings
On this tab it is possible to specify baseline correction, noise reduction and smoothing parameters for mass spectra

MS Spectral Bunching Peak Spectral Bunch Defines the number of spectra to be bunched at the apex
No Baseline Correction No baseline correction calculations will be performed
Peak Dependent Correction Allows specification of the number of spectra to be bunched
before peak start and after peak end in performing the
baseline correction
Fixed Correction Allows specification of 2 baseline segments independent of
the peak position to be used in the baseline correction
calculation
MS Noise Reduction Do Not Reduce Noise No noise reduction calculations will be performed

Chromeleon 7

Relative Threshold Allows masses below a specified percentage of the base peak
to be ignored
Fixed Threshold Limits spectra to only N largest mass intensities for a peak
MS Chromatogram Settings Mass Precision Defines the number of decimal places displayed by
Chromeleon and usable by the user
Mass Tolerance Allows masses below a specified value independent of the
peak to be ignored
Inhibit Integration for TIC Defines whether the TIC is integrated or not
Smoothing Defines the type and level of smoothing to be performed
5.3.12 MS Library Screening

On this tab it is possible to specify default parameters that will be used for both ad hoc (on demand) library searches, as well
as automatic library searches performed as part of data processing.

MS libraries to be searched (Checkbox List of libraries) When the box is checked next to a library in this list, that
library will be used as searched when a library search is
invoked.
Normal: Uses a standard pre-screen search filter. This is the
default search type.
Penalize Rare Compounds: Limits the impact of rare
compounds by reducing their match factors. This option is
effective only when you have selected a NIST Mass Spectral
Library (such as, mainlib). It has no effect on spectra in
internal NIST libraries or other commercial libraries.
Each reference spectrum in a NIST Mass Spectral Library
contains a record of other commercial libraries containing
information about the compound. A compound is considered
'rare' if it is present in a limited number of these libraries.
Similarity Simple: Finds a large set of spectra to compare with the
submitted spectrum. This search option is generally slower
than an identity search.
Hybrid: Uses a combination of the Simple and Neutral Loss
search types. When Hybrid is selected, the Search with Mol.
Weight edit box under Search Options is enabled. Enter an
estimate of the submitted spectrum's molecular weight.
Neutral Loss: Compares neutral losses of the submitted
spectrum with spectra in the library data. The neutral losses in
a spectrum are the mass differences between the molecular
ion and other major ions in the spectrum. For certain classes
of compounds, neutral losses can be a very characteristic
spectral feature. In a Neutral Loss search, Chromeleon
identifies the molecular ion of the submitted spectrum and
includes the molecular ion in the search, along with the
spectrum. Significant neutral losses of the submitted spectrum
are calculated and compared with the library data. Hits are
returned according to matches of the molecular ion and its
neutral losses. When Neutral Loss is selected, the Search
with Mol. Weight edit box under Search Options is enabled.
Enter an estimate of the submitted spectrum's molecular
Search options Search with Molecular Wt When a value is supplied, searches will be restricted to library
entries with the indicated molecular weight.
Reverse Search When checked, this parameter indicates that a reverse search
will be performed instead of a standard search
Thresholds Match Factor Defines the minimum match factor below which matches will
not be reported
Reverse Match Factor Defines the minimum reverse match factor below which
matches will not be reported

Chromeleon 7

Probability Defines the minimum probably below which matches will not
be reported
5.3.13 Peptide Table

Upon import of a Pinpoint workbook, the Peptide Table will be populated which is primarily read-only. The user has the
ability to delete an isotope of a peptide but cannot re-add deleted peptide isotopes. The fields displayed are described
below.
Name Description
Name Peptide sequence, including modifications. Duplicate names may exist if multiple charge states of the same
peptide sequence are imported.
RT Expected retention time of peptide
Charge Charge state of the peptide
Precursor Exact mass of the peptide assuming all atoms are of the most abundantly occurring isotope in nature
Isotope n Exact mass of isotopes from the monoisotopic mass to the least abundant mass. n is defined by the number
of isotopes for each peptide in the Pinpoint workbook.
5.3.14 QD Calibration
The “QD Calibration” tab is the area that shows all the global calibration settings and the list of calibration standards that are
used to quantify the peaks in the currently active chromatogram when using a QD detector. In this tab it is possible to
disable/enable the calibration points for specific peaks/channels. Additional options available are:

Mode Fixed The calibration standards from a selected sequence are used
for calibration. The other sequence is copied to the calibration
table in the processing method. You can update the calibration
any time, for example, after the other sequence has been
updated.
Total Calibration is performed using all valid calibration standard
samples of the sequence.
Additional For calibrating a sample, all calibration standard injections that
are listed before this sample in the sample list are used.
Group The calibration of a sample series from the sample list (for
example, samples 3 to 50) is performed based on the
calibrations standards listed directly before this series; for
example, no. 1 and 2. If this sample list includes further
standards, as for instance, no. 51 and 52, the following
samples, for example, 53 to 100, will be evaluated based on
these. The standard samples in lines 1 and 2 will no longer be
considered.
Bracketed Samples are evaluated based on all calibration standards
immediately surrounding. In case of a list containing two
samples, two calibration standards, two samples, two
calibration standards and so on, samples 1 and 2, located at
positions 3 and 4, are evaluated with standards 1, 2, 3, and 4,
located at positions 1, 2, 5, and 6. Samples 3 and 4 are
evaluated using the standards 3, 4, 5, and 6, located at
positions 5, 6, 9, and 10.
Standard Addition Calibration is performed using spiked and unspiked injections.
Curve Fitting Normal Selects normal dependent and independent variables for
calibration i.e. x-axis = amount, y-axis = measured value.
Inverted Selects inverted dependent and independent variables for
calibration i.e. x-axis = measured value, y-axis = amount.
Dual-Column Separate Mode N/A When this function is enabled it is possible to use only the
standards for the active column in tandem mode.
Origin of Standards for Fixed N/A Allows the user to select an external sequence for calibration.
Calibration On selection, all standards in the external sequence are copied
into the current sequence.

Chromeleon 7

Calibrate Using Normality N/A When enabled, the Concentration Unit (found on the
Component Table) is locked to the selected Normality unit.
5.3.15 MS Component Table Import

It is possible to create a MS component table by importing file types or searching through libraries. The import dialogue can
be opened by selecting any of the Component Table variant tabs in the processing method, then clicking the Import button
in the Studio Ribbon on the Processing Method tab.
The following file types are available:
Type Description
MS Raw Data Xcalibur raw data format containing an acquisition list in the data file header generated by ISQ, TSQ-8000,
and TSQ Quantum GC mass spectrometers and TSQ Quantiva and TSQ Endura LC mass spectrometers for
quantitative scan types.
Compound Data Store TraceFinder compound data store formats (Version 2, 3, 4 and 5)
NIST Library (See below)
Acquisition List Acquisition lists for quantitative scan types in the following formats:
ISQ and TSQ Series SQ and QqQ GCMS
TSQ Series LCMS
Exactive Series Inclusion/Exclusion lists
BioPharma Finder Peptide BioPharma Finder Peptide lists consisting of only one (1) protein and MS1 isotopes as well as multiple
List peptide and charge states can be imported into Chromeleon. Upon import, a component group for each
peptide consisting of a sum of all the peptide charge states and individual charge states will be created. A
component will be created for each summed peptide and peptide charge state. At the same time, theoretical
isotope distributions will be calculated and created for each charge state’s isotope.
BioPharma Finder Peptide lists are generated by BioPharma Finder version 3.0 and earlier
BioPharma Finder BioPharma Finder Peptide lists consisting of only one (1) protein and MS1 isotopes as well as multiple
Workbook peptide and charge states can be imported into Chromeleon. Upon import, a component group for each
peptide consisting of a sum of all the peptide charge states and individual charge states will be created. A
component will be created for each summed peptide and peptide charge state. At the same time, theoretical
isotope distributions will be calculated and created for each charge state’s isotope.
BioPharma Finder Peptide workbooks are generated by BioPharma Finder version 3.1 and later
Pinpoint Workbook Pinpoint workbooks consisting of only one (1) protein and MS1 isotopes as well as multiple peptide and
charge states can be imported into Chromeleon. Upon import, a component group for each peptide
consisting of a sum of all the peptide charge states and individual charge states will be created. A component
will be created for each summed peptide and peptide charge state. At the same time, theoretical isotope
distributions will be calculated and created for each charge state’s isotope.
Further, NIST format library directories can be searched to create a component table. The search is applicable to the TIC
channel and is applicable to full-scan type data. Chromeleon will parse each peak apex spectrum and match based on
NIST search. The highest probability hit is used to create the component, quantitation peak, and 2 confirmation peaks
based on the base peak and second and third most intense mass peaks.
5.3.16 MS Component Table Export

It is possible to export an MS component table into an acquisition table in the TSQ-8000 scan table and Exactive Series
inclusion/exclusion list format files for quantitative scan types. These files can then be opened for use in the TSQ-8000 and
Exactive Series MS method editor. The export dialog can be opened by selecting any of the Component Table variant tabs
in the processing method, then clicking the Export button in the Studio Ribbon on the Processing Method tab.
Data mapping is defined as follows:
5.3.16.1 TSQ-8000
Scan Table Column Chromeleon Component Table Column Comments

Name Name
RT Retention Time
Ion Polarity Polarity Filter Will be exported as ‘Positive’ if the value is ‘+’ and as
‘Negative’ if the value is ‘- ‘
Window Window

Chromeleon 7
Pre-width Window
Post-width Window
Mass Mass Range if Scan Type Filter (experiment type)
is SRM, otherwise Product Mass Range
Product Mass Product Mass Range if Scan Type Filter 25 is the default Product Mass value in the scan table to
(experiment type) is SRM, otherwise 25. identify SIM experiment type
Collision Energy CID Filter if Scan Type Filter (experiment type) is 8 is the default Collision Energy value in the scan table to
SRM, Otherwise 8 identify SIM experiment type
Peak Width Will be exported with value 5 as 5 is the default Peak
Width value in the MS scan table.
5.3.16.2 ISQ
Scan Table Column CM component Mapping Translation

Name Name
RT Retention Time
Polarity Polarity Filter or Polarity from imported data if the Will be exported as ‘Positive’ if the value is ‘+’ and as
Polarity Filter doesn’t exist ‘Negative’ if the value is ‘- ‘
Window Window
Pre-width Pre-width from imported data (not visible from UI)
Post-width Post-width from imported data (not visible from
UI)
Mass Product Mass (UI XIC Mass)
5.3.16.3 Exactive Series – SIM mode only
Inclusion List Column Chromeleon Component Table Column Comments

Mass[m/z] XIC Mass
Formula [M] Chemical Formula Will be exported as null if charge is null
Formula type N/A
Species N/A
CS [z] Charge
Polarity Polarity Filter Will be exported as ‘Positive’ if the value is ‘+’ and
as ‘Negative’ if the value is ‘- ‘
Start [min] Retention Time – Window The result will be in minutes
End [min] Retention Time + Window The result will be in minutes
NCE CID Filter Will be exported as null if the filter is not found
Comment Name and Chemical Formula and Comment Will be exported in the format of:
N=<Name>;F=<Chemical Formula>;<Comment>.
Note that if the item is a Confirming Ion then we
will add a postfix “_CFn” to the name where n is
the number of the current confirming ion in this
component.
5.3.16.4 TSQ Quantiva and TSQ Endura
5.3.16.4.1 SRM Scan Mode
Scan Table Column CM component Mapping Comments

Compound Name
Retention Time (min) Retention Time
RT Window (min) Window * 2
Start Time Retention Time - Window

Chromeleon 7
End Time Retention Time + Window

Polarity Polarity Filter If the filter is empty, export the value that was imported.
Precursor (m/z) Precursor
Product (m/z) XIC Mass
Collision Energy CID Filter If the filter is empty, export the value that was imported.
5.3.16.4.2 SIM Scan Mode

Compound Name
Center Mass (m/z) XIC Mass
5.3.16.4.3 Full Scan Mode

Scan Range (Da) XIC Mass Range
Scan Rate Imported value
Q1 (or Q3) Resolution Imported value
(FWHM)
Source Fragmentation SID Filter If the filter is empty, export the value that was imported.
(V)
5.3.16.4.4 QED Scan Mode

Compound Name
Product (m/z) XIC Mass
Intensity Threshold Export the imported value
5.3.16.4.5 Precursor Ion Scan Mode

Product (m/z) Precursor

Chromeleon 7
Product (m/z)
5.3.16.4.6 Product Ion Scan Mode

5.3.16.4.7 Neutral Loss Scan Mode

Neutral Loss (m/z) Imported value
5.3.17 Cobra Wizard

The Cobra Wizard helps to define the initial peak detection settings for a chromatogram. The following parameters are
defined by the Wizard:
Consider Void Peak Defines if the void volume should be considered when defining the peak detection.
Integration Area Definable by selecting the desired integration range.
Baseline Noise Range Defines the baseline noise range of the chromatogram.
Cobra Smoothing Width Definable by selecting the narrowest peak of interest or by choosing the Auto
setting.
Minimum Area Definable by selecting the smallest peak of interest or by choosing the Auto setting.
Injection Type Allows the settings to be restricted to a specific injection type.
Channel Allows the settings to be restricted to a specific injection type.
5.3.18 SmartPeaks
SmartPeaks allows for easy modification of the peak detection for unresolved peaks. When selected the user draws a box
over the peaks of interest. SmartPeaks then shows various peak detection options (Figure 20). The user selects the one
they want to have and clicks OK. SmartPeaks then inserts the detection parameters required to reach this integration into
the detection parameter table. This ensures that the parameters are applied to all injections in the sequence.

Chromeleon 7
Figure 20: SmartPeaks Wizard - Select Alternative

The following advanced options are available:

Effect starts with Peak Effect starts at the beginning of the first peak in the window.
Selection Effect starts at the start time for the window.
Chromatogram Effect starts at the beginning of the chromatogram.
Effect ends with Peak Effect ends at the end of the last peak in the window.
Selection Effect ends at the end time for the window.
Chromatogram Effect ends at the end of the chromatogram.
Restrict to current channel N/A Restricts the detection parameters to the current channel.
Restrict to current injection N/A Restricts the detection parameters to the current injection type.
type
5.3.19 Component Table Wizard

The component table wizard helps to setup or update the component table. The following settings can be made by the
wizard:

General Overwrite existing Overwrites the existing components (Only if component table already
components includes components).
Create and name Runs a spectral library search to identify components. When this option is
components according to selected, the name of the matching component in the spectral library is
spectral library screening applied to the identified component.
results
Time Range Use Auto Range Adds peaks detected in entire chromatogram to component table.

Chromeleon 7

From n to n [min] Adds peaks in the defined time range to component table.
Filter peaks N/A Defines which peaks to be added to component table
Apply to peaks with Area
Height
Relative Area
Relative Height
Greater than Defines comparison value.
Reference Spectrum Define Reference Spectrum Available options here are set in the processing method (see section
Using 5.3.6.1)
Enable peak tracking using Defines window type as “Spectrum and Time” or Spectrum only”
window type
Review N/A Allows reviewing of created component table. The following table columns
can be updated:
Name (see section5.3.2.1)
Retention Time (see section5.3.2.2)
Window (see section5.3.2.3)
Comment (see section5.3.2.13)
5.3.20 Layouts
It is possible to select a layout for the Processing Method. Each layout shows Processing Method tabs and panes, specific
to a task. The layouts consist of pre-defined subsets of processing method tabs as described in sections 5.3.1 through
5.3.12. Further each layout contains a Component Table variant consisting of a subset of columns described in section
5.3.2. Please refer to the respective sections for the general layout and component table variants for more information. The
following layouts are available:
Name Description
Qualitative Layout with all setting for qualitative analysis
Quantitative Layout with all setting for quantitative analysis
3D Qualitative Layout with all setting for qualitative analysis for chromatograms containing 3D Fields
3D Quantitative Layout with all setting for quantitative analysis for chromatograms containing 3D Fields
MS Quantitative Layout with all setting for quantitative analysis for chromatograms containing Mass Spectral data
All Settings Layout with all available processing method settings
Chromeleon 6 Layout according to Chromeleon 6 QNT editor
Basic Quantitative One-page layout showing most used options; detection parameters, and a component table containing name,
retention time, window and amounts.
QD Quantitative Layout with all settings for quantitative analysis for chromatograms containing QD data
5.4 Data Processing Category

The pane buttons on the “Data Processing Home” ribbon allow showing or hiding of panes. The following panes are
available:
• Chromatogram (see section 5.4.1)
• Calibration Plot (see section 5.4.2)
• Interactive Results (see section 5.4.9)
• Peak Properties (see section 5.4.3)
• Interactive Charts (see section 5.4.4)
• Contour/3D Plot (see section 5.4.5)
• UV-Vis Spectra (see section 5.4.6)

Chromeleon 7
• Fluorescence Spectra (see section 5.4.7)

• I-t Plot (see section 5.4.8)
• Injection Rack (see section 5.4.10)
• Fraction Tray (see section 5.4.11)
• Mass Spectra (see section 5.4.12)
• MS Components (see section 5.4.13)
• Tentatively Identified Peaks (see section 5.4.14)
• MS AutoFilters (see section 5.4.15)
5.4.1 Chromatogram Pane

The chromatogram view allows the user to graphically define processing commands for either the chromatogram or for the
whole sequence. Figure 21 shows a typical chromatogram view:
Figure 21: Chromatogram View in Chromatography Studio
5.4.1.1 Zooming and Navigating in the Chromatogram

The chromatogram view allows zooming and navigating in the chromatogram as required with the following options:
Automatic Tool When active it is possible to zoom into the chromatogram by dragging an area.
Additionally, other actions can be performed.
Zoom When active it is possible to zoom into the chromatogram by dragging an area.
Undo Zoom Reverts the recent zoom operation and returns to the previous view.
In addition, the following zoom operations are available:
Double Click on the signal axis Automatically resizes the chromatogram height to the highest peak currently visible.
Double Click on the retention axis Automatically resizes the chromatogram width to the complete duration of the
chromatogram.

Chromeleon 7
Signal axis zoom tools Shown when moving the cursor over the signal axis. The following functions are
available:
+ zooms into the chromatogram vertically
Autoscale Signal resizes the chromatogram height to the highest peak currently
visible
- zooms out of the chromatogram vertically
Retention time axis zoom tools Shown when moving the cursor over the retention time axis. The following functions
are available:
+ zooms into the chromatogram horizontally
Autoscale Time resizes the chromatogram to the complete duration of the
chromatogram.
- zooms out of the chromatogram horizontally
Full size button Shown when moving the cursor to the bottom left corner of the chromatogram plot.
Click the full-size button to autoscale both axes simultaneously.
Right Click select Full Size Automatically resizes the chromatogram height to the full size.
Right Click select Autoscale Automatically resizes the chromatogram height to the highest peak currently visible.
Right Click select Unzoom Reverts the recent zoom operation and returns to the previous view.
Holding down the right-hand mouse button and Zooms into the chromatogram area selected.
selecting an area of the chromatogram select Zoom
5.4.1.2 Graphical Entry of Integration Parameters

It is possible to graphically enter all detection parameters directly by right hand clicking on the chromatogram, selecting
“Insert Detection Parameter” and choosing the required parameter from the dialog presented. The retention time for the
commands is automatically entered as the retention time of the point on the chromatogram selected by the right hand click.
The most frequently used peak detection parameters are also available in the Processing ribbon from the “Insert” drop
button, see 5.4.1.8.
In addition, Chromeleon can automatically define detection parameter values based on the chromatogram. This is
performed by holding down the right-hand mouse button and selecting an area of the chromatogram. When this is done the
following options are available depending on the peak detection algorithm:
For Chromeleon 6:
Set Peak Slice & Sensitivity The peak slice and sensitivity are calculated based on the area selected.
Set Inhibit Integration Range The “Inhibit Integration” parameter is turned on at the retention time of the left side
of the window and turned off at the retention time of the right side of the window.
SmartPeaks Starts the SmartPeaks integration assistant (see 5.3.18).
For Cobra:
Set Baseline Noise Range The left side of the selected area is entered into the Processing Method as the start
of the baseline noise range; the right side is entered as the end respectively.
Set Inhibit Integration Range The “Inhibit Integration” parameter is turned on at the retention time of the left side
of the window and turned off at the retention time of the right side of the window.
SmartPeaks Starts the SmartPeaks integration assistant (see 5.3.18).

Chromeleon 7
5.4.1.3 Manual Integration

The chromatogram view allows integrating the chromatogram manually. The respective tools are selected either
automatically when the “Automatic” tool is active based on the cursor position or by explicitly selecting one of the following
manual integration tools:
Edit Baseline Tool Used to modify the baseline.
Edit Delimiter tool Used to move the peak start or peak end.
Insert Peak Tool Used to create a new peak.
Peak Type Changes the peak type into one of the following options:
- Main Peak
- Rider - Tangential at lower peak end
- Rider - Tangential at both peak ends
- Rider - Exponential
Shape shoulder Adds second peak below existing one.
Split peak Splits the peak at current mouse position.
Delete Peak Deletes the integration of the selected peak.
Delete All Peaks Deletes the integration of all peaks.
Remove Manual Integration Removes all manual integration from the chromatogram.
In order to retain manipulations made to a chromatogram, the changes must be saved. On saving the changes the
chromatogram view automatically shows that the chromatogram has been manually modified.
Note: any changes made to the detection parameters do not affect the modified chromatogram.
5.4.1.4 (Manual) Peak Identification

When a peak is selected it is possible to assign a component to the peak by creating a new component record or by starting
the Component Table Wizard. These options can be selected in the ‘Processing’ ribbon:
Figure 22: Processing Ribbon in the Chromatography Studio
Add Component Adds a new component named “Component X” to the component table and
automatically adds the peak retention time and window to the component table.
Component Table Wizard Start component table wizard (see section 5.3.19).
The Manual Peak Identfication page shows a list of all possible components for the currently selected channel.

Chromeleon 7
Figure 23: Component Assignment List

The component which is assigned to the currently selected peak is labeled with a bold font. The numbers in the second
column show the time distance in minutes between the retention time of the currently selected peak and the expected
retention time of the corresponding component. The number is formatted with enclosing brackets […] if the currently
selected peak is inside the retention window of the component. The following assignment icons may appear in the list:
Icon Description
The component is automatically assigned to some peak in the chromatogram. The component which is assigned to the currently
selected peak is formatted with a bold font.
The component is not assigned to any peak in the chromatogram.
The component is manually assigned. The component(s) which is(are) manually assigned to the currently selected peak is
formatted with a bold font.
The automatic component assignment can be changed manually.
Assign Component Assigns the component(s) selected in the list to the currently selected peak in the
chromatogram. Automatic assignment is automatically disabled for this peak and
the selected component(s).
If a new (component) name is entered in the edit field above the list you have the
choice to either create a new component record in the Processing Method or
assign a so-called arbitrary component name to the peak.
Remove Manual/Automatic Assignment Removes the manual/automatic component assignment of the currently selected
peak.
Remove All Manual Assignments Removes all manual component assignments of any peak in the current
chromatogram.
Assigning multiple components to the currently selected peak is also possible. In this case all components which should be
assigned need to be selected in the list pressing via the Ctrl-key and clicking the left mouse button. Manually assigned
component are considered any more for the automatic assignment in the current chromatogram.
5.4.1.5 Overlay
It is possible to overlay chromatograms from samples in the same sequence or from different sequences. It is also possible
to overlay chromatograms acquired using different channels including virtual channels (e.g. overlay a chromatogram
acquired at 254 nm with a chromatogram acquired at 280 nm).
5.4.1.6 Properties
The following chromatogram display options are available:
5.4.1.6.1 Plot Details

Axes Time Axis Displays a time axis on the chromatogram.
Signal Axis Displays a signal axis on the chromatogram.

Chromeleon 7
Font Allows the font type and size of the axes to be defined.
Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Frame Frame that is drawn around the plot area.
Axes Descriptions Axes Titles Applies titles to the chromatogram axes.
Units Displays units on the axes of the chromatogram.
Font Allows the font type and size of the axes titles to be defined
Grid Signal axis grid lines Applies horizontal grid lines to the chromatogram.
Time axis grid lines Applies vertical grid lines to the chromatogram
Orientation Horizontal Displays the chromatogram in the landscape orientation.
Vertical Displays the chromatogram in the portrait orientation.
Signal details Raw data points Shows the raw data points.
5.4.1.6.2 Time Axis

This section allows the user to define the scaling used for the time axis. The following options are available.

Share time axes If your chromatogram plot includes overlaid chromatograms
and you have selected a Stacked arrangement on the
Comparison page, you can select whether to use a common
(shared) time axis for the chromatogram stripes, or separate
time axes. The unit on the time axis is always identical for all
chromatogram stripes.
Select the Share time axis check box to display a single time
axis for all chromatograms (default). Clear the check box to
display separate time axes for each chromatogram.
If you have cleared the Share time axis check box, select the
chromatogram from the Settings for chromatogram plot list for
which the settings under Range (see below) shall apply.
Range Autoscale or Fixed Determines the method for selecting the range. Can be set to:
Autoscale or Fixed, Autoscale on Peak, or Fixed using
Autoscale on Peak Formula.
Fixed using Formula
Autoscale or Fixed From Defines the start time of the chromatogram. Either Auto or a
specific time can be selected.
To Defines the end time of the chromatogram. Either Auto or a
Autoscale on Peak Selected Allows the user to select the peak by Name, Greatest Height,
Greatest Area, Number, or Component Table Number
Width Defines the width by which to pad the selected autoscaled
peak range. This can be defined or set to Autosize width.
Fixed using Formula From Defines the start time of the chromatogram using a formula
To Defines the end time of the chromatogram using a formula
Time mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals
Major tick mark Defines the interval for major tick marks
Minor tick mark Defines the interval for minor tick marks
Time axis units Minutes (min) The units for the time axis are minutes.
Seconds (s) The units for the time axis are seconds.
5.4.1.6.3 Signal Axis

This section allows the user to define the scaling used for the signal axis. The following options are available:

Chromeleon 7

Signal Axis Settings for chromatogram Determines the signal axis for which to define the settings. To be
plot able to select between different signal axes, you have to load at
least one Overlay. In addition, two signal axes must be displayed.
Range for selected plot Autoscale or Fixed Determines the method for selecting the range. Can be set to:
Autoscale or Fixed, or Fixed using Formula.
Fixed using formula
Autoscale or Fixed To Defines the end value of the signal axis. Either Auto or a specific
time can be selected.
From Defines the start value of the signal axis. Either Auto or a specific
Fixed using Formula From Defines the start value of the signal axis using a formula
To Defines the end value of the signal axis using a formula
Autoscale in time range or peak Autoscale in visible time Determines the signal autoscale options for the current
range chromatogram. Following options are enabled only for the signal
scale mode ‘Autoscale or fixed’; Autoscale in visible time range,
Autoscale in fixed time range Autoscale in fixed time range, Autoscale on peak.
Autoscale on peak
Autoscale in visible time range N/A Calculates the signal minimum and / or maximum on the basis of
the current time range specified on the Time Axis properties page.
Autoscale in fixed time range From Custom start value to calculate signal minimum and / or maximum.
To Custom end value to calculate signal minimum and / or maximum.
Autoscale on peak Selected Calculates the signal minimum and / or maximum on the basis of
the range between peak start and end time. Following peak
selection modes are available; by name, by greatest height, by
greatest area, by number, by component number.
5.4.1.6.4 Title
This section defines the caption that will be displayed in the chromatogram header. Left, middle and right captions can be
selected either based on simple text values or on user-defined formulas. Also defines the legend in the bottom left corner of
the chromatogram when several chromatograms are overlaid. The formula can be based on variables from the following
sections:
• Global Functions (7.1)
• General (7.2)
• Sequence (7.3)
• Injection (0)
• Audit Trail (see section 7.5)
• Preconditions (see section 7.6)
• Chromatogram (7.8)
• Processing Method (7.20)
• Instrument Method (7.30)
• Custom Formulas (5.7.27)
Note: If a chromatogram is manually integrated the text “[manipulated]” is always shown in the left caption.
In addition, the following options are available:

Draw titles Displays chromatogram titles.
Font Allows the font type and size of the titles to be defined

Chromeleon 7

Left title Draw left title Displays the left part of the title.
When checked the left part of the title can be defined based on
formulas as described above.
Middle title Draw middle title Displays the middle part of the title.
When checked the middle part of the title can be defined
based on formulas as described above.
Right title Draw right title Displays the right part of the title.
When checked the right part of the title can be defined based
on formulas as described above.
Legend Draw Legend Displays legend to the left of the chromatogram when several
chromatograms are overlaid.
When checked the legend can be defined based on formulas
as described above.
5.4.1.6.5 Peak Characterization

This section defines how detailed peaks are characterized in the chromatogram plot. The following options are available:

Peak delimiter Shows the peak delimiters.
Delimiter Allows defining color and line style for peak delimiters.
Separation Allows defining color and line style for the separation drop line.
Baseline Shows the baseline.
Main peak Allows defining color and line style for the baseline under a
main peak.
Rider peak Allows defining color and line style for the baseline under a
rider peak.
Peak tangents Shows the peak tangents.
Allows defining color and line style for peak tangents.
Draw peak width at Shows peak widths.
Peak widths
Allows defining color and line style for peak widths.
Draws a line at the given height. Defaults heights are 5%,
10%, 50%, but are user definable
Peak Highlight Do not highlight any peaks The identified peak will not be shaded unless it has the focus
Highlight all identified peaks All identified peaks will be shaded in all plots
Highlight all detected peaks All detected peaks will be shaded in all plots
5.4.1.6.6 Peak Label

This section defines how peaks should be labeled. The following options are available:

Identified peaks Label identified peaks Labels all identified peaks with details generated by the user-
defined formula.
(Formula) The formula can be based on variables from all the areas
Unidentified peaks Label unidentified peaks Labels all unidentified peaks with details generated by the
user-defined formula.
Label style Font Defines the font for peak labels.
Rotation Defines the angle the peak label is shown at.
5.4.1.6.7 Peak Purity

This section defines plot options for peak purity and peak match.

Chromeleon 7

Peak Purity Index Overlay peak purity index Shows the peak purity index in the chromatogram plot.
Line Style Allows defining line color, width and style for the peak purity
index.
Peak Match Overlay peak match factor Shows the peak match factor in the chromatogram plot.
Line Style Allows defining line color, width and style for the peak match
factor.
5.4.1.6.8 Peak Windows

Formulas used in this section can combine variables from the following categories:
• Global (7.1)
• General (7.2)
• Sequence (7.3)
• Injection (0)
• Component (7.28)
• Unidentified Peak Group (7.29)

Component table windows Show component table windows Displays peak windows for components from the component
table (dotted lines indicating the width of the retention window
for the peak). Note: peak windows allow the retention time and
retention window of peaks to be adjusted graphically.
(Formula) Labels all peak calipers for identified peaks with details
generated by the user-defined formula.
Unidentified peak group windows Show unidentified peak group Displays peak windows for unidentified peak groups.
windows
(Formula) Labels all peak windows for unidentified peaks with details
Other options Show all peak window drop lines Displays dotted lines for all peaks, not only the currently
selected peak.
Font Defines the font for peak windows.
5.4.1.6.9 Comparison
This section defines how chromatogram overlays are displayed. The following options are available:

Arrangement Overlaid All overlaid chromatograms are shown in one window.
Stacked All overlaid chromatograms are shown in stacked windows.
Grouped by detector All overlaid chromatograms are grouped by detector.
Overlay order Sorted by injection list order All overlaid chromatograms are identical to the order of
injections and channels in the Navigation Pane.
Current chromatogram always on Currently selected chromatogram is displayed in front of the
top other chromatograms.

Chromeleon 7

Offset Time Offset Offsets the overlaid chromatogram by the % time value
selected.
Signal Offset Offsets the overlaid chromatogram by the % signal value
selected.
Overlay Overlay with peak characterization If selected the peak characterization settings such as peak
names, peak delimiters or the baseline apply not only to the
active chromatogram but also to all overlaid chromatograms.
Overlay with right signal axis. If selected the overlaid chromatogram is measured against a
right signal axis.
Mirror last overlaid injection Mirrors the chromatogram that was added to the overlay last
on the time axis.
Normalization Normalize signal Normalizes the signal against the reference peak.
Peak Allows specification of the reference peak
Retention time Allows specification of the retention time to be used for
normalization
Normalize time Allows to normalize the signal in x direction either by shifting or
stretching all chromatograms so that the retention time of the
selected component matches for each overlaid chromatogram.
First peak Allows specification of the start peak for normalization
Second peak Allows specification of the end peak for normalization
Normalize signal Off No signal normalization
Peak Normalizes overlaid signal to height of specified peak
Retention time Normalizes overlaid signal to height of a specific data point
Full range Normalizes overlaid signal to maximum peak height
Normalize time Off No normalization by time
Shift to peak Shifts the overlaid chromatogram to overlay a specific peak
Stretch between start and peak Stretches the overlaid chromatogram between the start and
specified peak
Stretch between two peaks Stretches the overlaid chromatogram between the two
selected peaks
Stretch between start and end Stretches the overlaid chromatogram between the start and
end, in order that the run times match
5.4.1.6.10 Events
This section allows defining which events that occurred during the data acquisition or data processing are displayed on the
chromatogram. The following options are available:

Detection Parameters N/A Indicates the Detection Parameters.
Gradients Show gradients Displays the corresponding gradient profile.
Line style Allows to define color, width and line style for the gradient
profile.
Dwell time Defines the dwell time. This will draw a gradient profile that is
in accordance with the retention time.
For this device only Allows to select the device for which the gradients should be
shown. By default, gradients are displayed for all devices.
Signal parameters N/A Displays signal parameters in the chromatogram.
Triggers N/A Hide or show triggers from the instrument method in the
chromatogram.
Manual commands N/A Displays manual commands in the chromatogram.
Errors N/A Displays errors in the chromatogram.
Label Style Label events Displays event labels in the chromatogram.

Chromeleon 7

Font Defines the event label font.
5.4.1.6.1 Fraction Tubes

This section defines how fraction tubes should be displayed. The following options are available:

Tubes Show tubes Displays the tubes collected
Label tubes Displays a label for the tube based on a formula using
Chromeleon Report Variables
Fractions Show fractions Displays the fractions collected
Hide tubes inside fractions Removes distinctions between tubes collected as part of the
same fraction
Label fractions Displays a label for the fraction based on a formula using
Label Style Font Allows the font type and size of the labels to be determined
Rotation Allows the orientation of the label to be determined
Alignment Allows the location of the label to be determined
5.4.1.6.2 MS Quantitation Channel

This section defines special plot and display options to be applied when the MS Quantitation trace is displayed.

Trace visualization Trace offset If selected, each XIC is plot with a vertical offset compared to
the previous XIC; otherwise, all XICs are plotted on a common
using their true y-axis values
Show only display range of If selected, the XIC plot range is limited to the display range as
extracted ion trace defined in the component table of the processing method.
If not selected, the full-time range of the XIC is plotted.
Use alternating colors If selected, the XICs are drawn using a rotating color palette
as defined in the Line and Fill Styles tab.
If not selected, the XICs are drawn using the primary plot
color, as defined in the Line and Fill Styles tab.
Show peak characterization If selected, the MS Quantitation plot is annotated with peak
characterizations (peak delimiters, peak tangents, baseline
and width.)
Label traces Label quantitation peaks Shows or hides the XIC peak labels
Label style Alignment Defines if the peak labels should be placed above the peak
apex or at the lower right of each peak trace.
Draw Frames If selected, a box is drawn around the peak labels
Font Defines the font for peak labels.
5.4.1.6.3 Spectral Thumbnails

This section defines how spectral thumbnails should be displayed. The following options are available:

Show Thumbnails Automatic Displays the thumbnails only when the UV-Vis Spectra Plot is
also displayed.
UV Always displays the thumbnails if UV spectral data are
available.

Chromeleon 7
Fluorescence Always displays the thumbnails if fluorescence spectral data

are available.
Amperometry Displays the thumbnails of any existing I-t plots in all channels.
MS Displays the thumbnails of any existing MS plots in all
channels.
None Don’t display any UV spectra thumbnails in the
chromatogram.
Thumbnails Size Width Defines the width of the thumbnail in mm.
Height Defines the height of the thumbnail in mm.
Range Bars Draw average range bars Marks and labels the ranges from which bunched spectra
were taken in the chromatogram. The number of spectra
averaged within a range is displayed in parenthesis.
5.4.1.6.4 Line & Fill Styles

This section allows a consistent color scheme for the objects in the chromatogram plot to be defined. The following items
can have their line color defined:
• Chromatograms 1-8 • Peak tangents • Manual Commands
• Temporary scan extract • Peak width • Errors
• Peak delimiter • Raw data points • Peak purity index
• Peak separation • Detection parameters • Peak match index
• Baseline • Gradients • Tubes
• Rider baseline • Signal Parameters • Fractions
• Free baseline • Triggers • Selected peak
The following items can have their fill color defined:
• Background • Peak label • Event label
• Detection parameter label • Tube label • Tubes
• Fractions • Selected peak • Selected peak label
5.4.1.6.5 Interactive Settings

This section defines the interactive settings in the chromatogram. The following options are available:
Maximum hit test distance Specify the distance when the shape of the mouse pointer changes when you
approach an object in the chromatogram plot.
Show overview plot When this check box is selected, the miniature overview of the chromatogram plot
is displayed when zooming into the chromatogram.
Show popup controller When this check box is selected, the full-size button, vertical and horizontal zoom
toolbars on the chromatogram axes are visible.
Visualize selections When this check box is selected, visualization of selected objects, such as a
selected peak, is enabled.
Highlight selected chromatogram Enables or disables the highlighting of the selected chromatogram.
5.4.1.6.6 Manual Peak Identification

This section allows manual peak identification (also see 5.4.1.4). The “Currently selected peak” section contains read only
fields, which show properties of the currently selected peak. The “Assign component or add arbitrary name for selected
peak” section contains the following options:
Component List of peaks in the component table. This filed also gives the possibility to enter an
arbitrary name.
Assign Component Manually Forces the peak to be identified with the selected component from the component
table.

Chromeleon 7
Assign Arbitrary Name Assigns arbitrary name (entered in the Component box) to the peak.
Remove manual assignment Removes the manual component assignment of a peak.
Remove all manual assignments Removes all manual component assignments of any peaks in the current
chromatogram.
5.4.1.7 Hotkeys
It is possible to navigate around the chromatogram using hotkeys. The following hotkeys are supported by Chromeleon:
Key Function
Left Cursor / 4 on Number Pad Scroll time axis left by 5%.
Right Cursor / 6 on Number Pad Scroll time axis right by 5%.
Up Cursor / 8 on Number Pad Scroll signal axis up by 10%.
Down Cursor / 2 on Number Pad Scroll signal axis down by 10%.
Home Scroll to the chromatogram start. No scale changes.
End Scroll to the chromatogram end. No scale changes.
/ (Divide) Zoom time axis out by 25 %.
* (Multiply) Zoom time axis in by 20 %.
- (Minus) Zooms signal axis out by 25 %.
+ (Plus) Zooms signal axis in by 20 %.
5 (5 on number pad) Returns the chromatogram to full scale on the time and signal axes.
Ctrl together with Left Cursor Selects the previous peak.
Ctrl together with Right Cursor Selects the next peak.
Space Changes to next mouse tool (Automatic → Delimiter → Baseline → Detection
Parameter → Insert Peak → Spectra Tool).
Delete Delete selected peak.
Ctrl together with Y Redo the last peak manipulation
Ctrl together with Z Undo the last peak manipulation.
Alt together with Backspace Undo the last peak manipulation.
F4 Replaces active chromatogram with next chromatogram.
Shift together with F4 Replaces active chromatogram with previous chromatogram.
F1 Shows context sensitive help.
5.4.1.8 Detection Parameters

The “Insert” button on the “Processing” ribbon allows the following detection parameters to be created at the retention time
position of the cursor:
• Inhibit Peak Detection • Fixed Baseline Point • Minimum Width
• Baseline Type Valley to Valley (On) • Minimum Area • Baseline Noise Range
• Detect Negative Peaks (On) • Minimum Height • Cobra Smoothing Width
In addition, “Other Parameter” shows a dialog to choose from a complete list of all available detection parameters.
5.4.1.9 Export Chromatogram

The chromatogram can be exported to a text file using the context menu command “Export Chromatogram (Text format)”.
The command launches a dialog with further options (Figure 24).

Chromeleon 7
Figure 24: Chromatogram Export Option Dialog Box


Destination Clipboard Exports a textual description of the chromatogram data or raw
data into the clipboard.
File Exports a textual description of the chromatogram data or raw
data into a file.
Options Chromatogram data Exports only the chromatogram data.
Raw data Exports chromatogram data including raw data.
Additionally, the chromatogram plot can be copied into the clipboard as an image using the Ctrl + C hotkey.
5.4.1.10 Arithmetic Combination

The Arithmetic Combination combines two existing channels, from the same or different injections (including an injection in
another Data Vault), using the arithmetic operations: add, subtract, multiply, and divide.
Figure 25: Channel Processing Arithmetic Combination Dialog Box


Channel A Original channel The original channel (read-only) that will be used as Channel
A in the arithmetic operation.
Factor A User defined factor with which Channel A is multiplied.
Channel B Current channel A selectable channel from the current sequence that will be
used as Channel B in the arithmetic operation.
Fixed channel A channel from another data vault that will be used as
Channel B in the arithmetic operation.

Chromeleon 7
Factor B The factor with which Channel B is multiplied.

Output Operation The arithmetic operation that will be used to combine the data
points in Channel A and Channel B: A+B, A-B, A*B, A/B, B/A.
Result channel Name for the new channel.
Apply to the following injections Processing action options: current, selected/pinned, all, type.
within the current sequence
Overwrite existing channels Option to overwrite a channel if it already exists in the current
sequence.
5.4.1.11 Copy Channel

The chromatogram channel can be copied using the context menu command “Copy Channel”. This command is available
on the Navigation Pane; Under Channels, right-click the channel that you want to copy, or on the chromatogram plot, right-
click in the chromatogram, and then click Copy Channel.
Figure 26: Chromatogram Copy Channel Dialog Box

Original channel The name of the original channel (read-only) to be copied.
Apply to the following injections within the current Processing action options: current, selected/pinned, all, type as either Unknown,
sequence Blank, Check Standard, Calibration Standard, Matrix, Spiked and Unspiked.
Overwrite existing channels Option to overwrite a channel if it already exists in the current sequence.
Note: If the chromatogram was manually modified before the channel was copied, any modifications will be copied too.
5.4.1.12 Derivatives
The derivative processing action outputs the first or second derivative of an existing channel to a new channel.
Figure 27: Channel Processing Derivatives Dialog Box


Chromeleon 7
Original channel The original channel (read-only) that will be used to calculate the first or second
derivative.
Derivative First and second derivative options.
Apply to the following injections within the current Processing action options: current, selected/pinned, all, or specify injection type as
sequence either Unknown, Blank, Check Standard, Calibration Standard, Matrix, Spiked and
Unspiked.
5.4.1.13 Power Law

Applies a power factor to an existing channel such that the data points are raised by a power of between 1.0 and 2.0, with
the results being output to a new channel (the original channel remains unchanged).
Figure 28: Channel Processing Power Law Dialog Box

Original channel The original channel (read-only) to which the power factor will be applied.
Power factor Power factor between values of 1.0 and 2.0.
Unspiked.
5.4.1.14 Smooth Channel

Smoothes the data in an existing channel. The smoothing process applies a digital filter (smoothing algorithm) to the
channel data to reduce signal noise.
Figure 29: Channel Processing Smooth Channel Dialog Box


Chromeleon 7
Original channel The original channel (read-only) to which the smoothing process will be applied.
Filter type Smoothing process filters: Moving Average, Olympic, Savitzky-Golay, Gaussian.
Filter size The number of input data points used to generate each output data point.
Unspiked.
5.4.2 Calibration Plot Pane

The calibration view can be modified to display calibration curves in various different ways. In addition, zooming into the
calibration curve is possible.
Double clicking a calibration point shows the associated chromatogram in the chromatogram pane (if shown) and also
selects the respective line in the interactive result tables.
Figure 30 shows a typical calibration curve view.
Figure 30: Calibration Plot View

The following calibration curve display options are available.
5.4.2.1 Scale

Proportional n.a. If selected, changes are applied to all calibration plots.
Amount Axis From Defines the start value of the amount axis.
To Defines the end value of the amount axis.
Autoscale If selected the full range is shown and the values are not
considered.
Logarithmic Scale Applies the logarithmic scale to the amount axis.
Fixed intervals of tick marks Customizes the interval of tick marks via typing or selecting a
number in the Major tick mark and/or Minor tick mark boxes.
Response Axis From Defines the start value of the response axis.
To Defines the end value of the response axis.
considered.

Chromeleon 7

Logarithmic Scale Applies the logarithmic scale to the response axis.
Apply log-log linear transformation n.a. Applies a log-log linear transformation to the current plot.
5.4.2.2 Frame & Axes

Axes Amount Axis Displays an amount axis on the calibration plot.
Response Axis Displays a response axis on the calibration plot.
Fonts Allows the font type and size of the axes to be defined.
chromatogram plot.
Frame Allows the calibration curve frame to be removed.
Axis Titles Axis Titles Applies titles to the calibration plot axes.
Units Displays units on the axes of the calibration plot.
Fonts Allows the font type and size of the axis titles to be defined.
Grid Horizontal grid lines Applies horizontal grid lines to the calibration plot.
Vertical grid lines Applies vertical grid lines to the calibration plot.
5.4.2.3 Title
This section defines if titles are displayed and how titles should be displayed:

Draw titles Shows a title for the calibration plot.
Font Allows the font for the calibration plot title to be defined.
Use default When checked left part of the title is shown as in Chromeleon
7.2.
When not checked the left part of the title can be defined
based on formulas in the edit field.
Center title Draw center title Displays the middle part of the title.
Use default When checked middle part of the title is shown as in
Chromeleon 7.2.
When not checked the middle part of the title can be defined
Use default When checked right part of the title is shown as in Chromeleon
7.2.
When not checked the right part of the title can be defined
5.4.2.4 Options

Check Standard & Current Injection Draw check standard injection Draws points for check standard injection points on the
points calibration plot.
Draw level tolerance lines Displays concentration level tolerance lines on the calibration
plot.

Chromeleon 7

Draw response/amount Draws a horizontal line from the from the response axis
quantification lines of current (response value of the current injection). Where the line hits
injection the calibration curve, a vertical line is drawn to the amount
axis.
Confidence Interval Draw upper and lower confidence Draws the upper and lower confidence limits of the calibration
limits curve.
Upper probability, Lower The confidence probability to be used when calculating the
probability confidence limits. The following values can be selected:
•95 %
•97.5 %
•99 %
•99.5 %
•99.9 %
•99.95 %
•99.995 %
Draw Hubaux-Vos detection limit Draws the Hubaux-Vos detection limits for the calibration
curve.
5.4.2.5 Line & Fill Styles

This section allows a consistent color scheme for the objects in the calibration plot to be defined. The following items can
have their line color defined:
• Grid • Markers • Original markers
• Axes • Selected marker • Hubaux-Vos lines
• Calibration curve • Disabled markers • Quantification lines
• Confidence interval curves • Check standard markers
• Prediction limit curves • Check Standard outlier markers

• Background
5.4.2.6 SmartLink
Group Sub Parameter Description

Link to Chromatogram N/A Links the object to the chromatogram.
Multiple Peak Selection When selected, the peaks that are selected in the chromatogram
plot define which peaks are displayed in the calibration plot.
Zoom Area When selected, the zoom area of the chromatogram plot defines
which peaks are shown in the calibration plot.
5.4.2.7 Interactive Settings

This section defines what optional zoom/unzoom tools are displayed on the calibration plot.
Always display the selected plot first Displays the calibration plot of the selected peak in the chromatogram first.
Show overview plot When this check box is selected, the miniature overview of the calibration plot is
displayed when zooming into the calibration plot.

Chromeleon 7
5.4.3 Peak Properties Pane

The peak properties pane offers 3 property pages to view the results and/or edit properties of the currently selected peak or
component. The 3 property pages are
• Peak: Lists configurable results of the currently selected peak
• Components: Lists the properties of the currently selected component
• MS Detection: Lists and allows to edit the MS detection settings for so-called Extracted Ion Chromatograms (XIC,
see 5.3.2.21 for details)
5.4.3.1 Peak
In the upper part of the property page “Peak” a configurable number of results is shown for the currently selected peak in the
chromatogram (see Figure 31 below).
Figure 31: Peak Properties Pane – Page “Peak”

The list of Property Name / Value pairs can be configured. The corresponding settings are stored in the currently active View
Settings. The following options are available:
Edit Opens the result formula dialog to edit the current result formula, its format and the label (Property Name column). The
corresponding peak result is shown in the currently selected row of the Property Name / Value list.
Insert Opens the result formula dialog to select a new formula, its format and the label (Property Name column). A new result row
is inserted at the currently selected row into the Property Name / Value list.
Delete Removes the currently selected result row from the Property Name / Value list.
Append Opens the result formula dialog to select a new formula, its format and the label (Property Name column). A new result row
is appended to the Property Name / Value list.
Move Up Moves the currently selected row one position up in the Property Name / Value list.
Move Down Moves the currently selected row one position down in the Property Name / Value list.
The lower part of this page allows to manually modify the automatic component assignment of the currently selected peak.
The corresponding user interface and options are identical to the corresponding options in the Manual Peak Identification
Page in the properties dialog of the Chromatogram Pane (see 5.4.1.4 for details).
5.4.3.2 Component
The property page “Component” lists the properties for the currently selected component. This is especially useful if the
component table of the Processing Method Editor is not open. It is possible to edit the properties. The changes will be
transferred to the component table. The following properties are listed (see section 5.3.2 for descriptions):

Chromeleon 7
• Name • Ret.Index • Mol.Mass

• Channel • Conc.Unit • CAS
• Comment • Peak Type • Chem.Formula
• Factor • Up.Conf.Prob. • Ref.Mass.Spec.Settings
• Eval.Type • Low.Conf.Prob. • Extr.Ion.Chm
• Cal.Type • Ref.UV.Spec. • Charge
• Stand.Meth. • Match Crit • Requires Reference Peak
• Ret.Time • Threshold • RTS Ratio Tolerance
• Window • WL-Range • Peak Group(s)
• Prev.Retention • Spec.Deriv.
• Left Limit • Rel.Max.Dev.
• Right Limit • Check Extr.
5.4.3.3 MS Detection
The MS Detection page is only present for Extracted Ion Chromatograms (XIC, see 5.3.2.21 for details). It shows the MS
Detection settings for the currently selected XIC and allows also to edit them in the section below the Detection Settings
label (see Figure 32 below).
Figure 32: Peak Properties Pane – Page “MS Detection”

Component Show the name of the currently selected component and allows the select the next or
previous one of the component table.
XIC Shows the currently selected XIC of the component and allows the select the next or
previous one, i.e. MS Quantitation Peak or MS Confirmation Peak(s).
Use Processing Method • Shows the MS Detection settings of currently selected XIC in the Detection
(applied for all injections) Settings below if the MS Detection settings are used from the Processing Method.
• Selects to use the MS Detections settings from the Processing Method instead
injection specific ones.
Use MS default Shows or selects to use the MS default detection settings which are stored in the
detection settings Processing Method and applied for all injections which have assigned the current
Processing Method.
Apply… Opens up a dialog to (bulk) apply the MS default detection settings to some or all
components and XICs.
Use XIC specific Shows or selects to use XIC specific detection settings which are stored in the
detection settings Processing Method and applied for all injections which have assigned the current
Processing Method.

Chromeleon 7

Copy and apply... Opens up a dialog to (bulk) copy and apply the currently selected XIC specific detection
settings to some or all components and XICs.
Use Injection Specific • Shows the MS Detection settings of currently selected XIC in the Detection
detection settings Settings below if the MS Detection settings are only valid for the currently selected
injection.
• Selects to use the MS Detections settings for the currently selected injection only
instead of the MS Detection settings stored in the Processing Method.
5.4.4 Interactive Charts Pane

The Interactive Charts pane allows the user to instantly display charts of chromatography results, making the results easy to
interpret at a glance. Interactive Charts can be used to display the values of any appropriate variable across a range of
injections, or across the peaks within an individual injection.
Selecting any data point in an Interactive Chart updates the selections in all the other panes, so the underlying data of a
point of interest can be immediately accessed. The Interactive Chart can be modified to display Chromeleon report formulas
in various different ways. In addition, zooming into the calibration curve is possible. Figure 33 shows an Interactive Chart
Pane.
Figure 33: Interactive Charts view in the Chromatography Studio

There are two types of Interactive Charts:
• Peak Charts: charts displaying chromatography results of the peaks within a chromatogram.
• Injection Charts: charts displaying chromatography results of the injections in a (virtual) sequence.
When inserting a new chart, the following templates are available:
Retention Time Injection chart: displays retention time trend of a selected peak.
Column Performance Injection chart: displays theoretical plates, resolution and asymmetry of a selected
peak.
Component Area Injection chart: displays area of a selected peak.
Rel. Peak Area Peak chart: displays relative peak area of peaks in chromatogram.
Check Standard Injection chart: displays check standard amount of a selected peak.
Amount Deviation Injection chart: displays deviation for the selected peak of the calculated amount in
calibration and check standards against the amount entered in the amount
columns of the processing method.
Electrolytic Devices Injection chart: displays status of electrolytic devices.

Chromeleon 7
Isotopic Distribution Injection chart: displays peak area distribution of each isotope across all injections.
If a summed peptide is selected, peak area ratios are displayed against the most
abundant observed isotope peak area. If a peptide charge state is selected, peak
area ratios are displayed against a theoretical isotopic distribution.
Isotopic Ratios Injection chart: displays relative intensities of isotopes normalized to a sum total of
100% across all injections. When the summed peptide is selected, the plotted data
is for observed data only. When a peptide charge state is selected, the plotted
data consists of both theoretical distribution as well as observed distribution.
The following Interactive Chart display options are available.
5.4.4.1 Data Settings

Horizontal Axis Variable n.a. Displays horizontal axis variable that can be user defined
based on all report formulas from all the areas detailed in
section 7.
Note: This option is only available for scatter charts.
Variables Chart Type Defines chart type. All chart types from section 5.4.4.2 are
available.
Chart Variable Defines chart variable that can be based on all report formulas
from all the areas detailed in section 7.
Style Defines color, line style and symbol type for the chart.
Notes:
For the bubble chart type an additional Circle Diameter parameter is displayed to define the bubble diameter.
For the High Low chart type two additional lines are displayed, to define formulas used for start and end values.
For each selected Control Chart option (5.7.17.13) a line is displayed to define the formula.
5.4.4.2 Chart Type

The following chart types are available:
5.4.4.2.1 Scatter
• Scatter with only points • Scatter with points & lines • Scatter with points & splines
• Scatter with Lines • Scatter with Splines
5.4.4.2.2 Line
• Line • Line with points • Spline with points
• Spline
5.4.4.2.3 Column
• Column • Stacked column (100%) • Stacked column 3D
• Stacked column • Column 3D • Stacked column (100%) 3D
5.4.4.2.4 Area
• Area • Stacked area (100%) • Stacked area 3D
• Stacked area • Area 3D • Stacked area (100%) 3D
5.4.4.2.5 Pie & Doughnut

• Pie • Pie 3D • Doughnut 3D

Chromeleon 7
• Doughnut
5.4.4.2.6 Miscellaneous
• Bubble • Range Area • Column range 3D
• High Low • High Low 3D • Range area (100%) 3D
• Column Range
5.4.4.3 Filter Options – Injection Charts

Include Injection Types Unknown Displays values from unknown injections.
Calibration Standard Displays values from calibration standard injections.
Check Standard Displays values from check standard injections.
Matrix Displays values from matrix blank injections.
Blank Displays values from blank run injections.
Spiked Displays values from spiked injections.
Unspiked Displays values from unspiked injections.
Custom Conditions And (Any field from the injection Restrict the data points shown based on comparing the selected
list – including user defined variable with a user-defined value and using the following logical
columns) arguments:
Is equal to (=)
Is not equal to (<>)
Is larger than (>)
Is smaller than (<)
Is larger than or equal to (=>)
Is smaller than or equal to (=<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Is not during previous
And [Any field from the injection As for the previous parameter.
list – including user defined
columns]
5.4.4.4 Filter Options –Peak Charts

Include Peaks Identified Peaks Shows all peaks that have been identified.
Unidentified Peaks Shows all peaks that have not been identified.
Undetected Components Includes rows for those components of the Component table
(in the Processing Method) that have not been detected in the
current injection.

Chromeleon 7

Custom Conditions And (Any field from the injection Restrict the data points shown based on comparing the
list – including user defined selected variable with a user-defined value and using the
columns) following logical arguments:
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
And [Any field from the injection As for the previous parameter.
columns]
5.4.4.5 Grouping Options – Injection Charts

Sort the injections according to Injection Number Sorts the injections according to injection number.
Evaluation of this formula Injections are grouped by the user-defined formula based on
all report formulas from all the areas detailed in section 7..
Ignore case comparing text results Ignore case when comparing text results.
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6.
Group Labels Displays group labels in interactive charts.
5.4.4.6 Grouping Options – Peak Charts

Sort the peaks according to Peak Number Sorts the peaks according to peak number.
all report formulas from all the areas detailed in section 7.
5.4.4.7 Title

Draw titles Displays interactive chart titles.
Font Allows the font type and size of the titles to be defined.

Chromeleon 7

section 7.
section 7.
section 7.

• Global Functions (7.1) • Peak Calibration (7.11)
• General (7.2) • Peak Purity and Identification (7.12)
• Sequence (7.3) • Processing Method (7.20)
• Injection (0) • Component (7.28)
• Audit Trail (7.5) • Unidentified Peak Group (7.29)
• Preconditions (7.6) • Instrument Method (7.30)
• Chromatogram (7.8) • Custom Formulas (5.7.27)
• Peak results (7.10)

Axes Horizontal Axis Displays a horizontal axis on the interactive chart.
Vertical Axis Displays a vertical axis on the interactive chart.
Axes Description Draw Axes Title Applies titles to the interactive chart axes.
Units Displays units on the axes of the interactive chart.
Group labels Displays the group labels.
Horizontal Axis Label Formula Labels horizontal axis with details generated by the user-
defined formula based on all report formulas from all the areas
Grid Horizontal grid lines Applies horizontal grid lines to the interactive chart.
Vertical grid lines Applies vertical grid lines to the interactive chart.
5.4.4.9 Horizontal Axis

Range From Defines the start value of the horizontal axis. Either Auto or a
specific value can be selected.
To Defines the end value of the horizontal axis. Either Auto or a
5.4.4.10 Vertical Axis

Settings for axis Determines the vertical axis for which to define the settings. To be
able to select between different vertical axes, you have to have at
least two chart variables.

Chromeleon 7

Range From Defines the start value of the vertical axis. Either Auto or a specific
To Defines the end value of the vertical axis. Either Auto or a specific
5.4.4.11 Data Labels


Data Point Labels Draw Data Point Labels Labels all data points with details generated by the user-
defined formula.
Font Defines the font for data point labels.
Chart variable name Displays the (short) name of chart variable in the label.
X value Displays x value of the data point (for scatter charts only).
Y value Displays y value of the data point.
Report Formula The formula can be based on variables from all the areas
Legend Show Legend Displays legend in the upper right corner of the chart. Options:
Inside plot area
Outside plot area
5.4.4.12 Statistics
Mean Displays a horizontal line at the average value of the data set.
Linear trend line Displays a linear trend line of the data set.
Show trend line formula includes the linear formula for the trend line in its data label
1s (Mean +/- 1 Std. Deviation) Displays two horizontal lines at the 1s level of significance value of the data set.
Font Defines the font for the labels.
5.4.4.13 Control Chart
Upper Limit Displays the line of the defined upper limit value or report formula.
Target Displays the line of the defined target value or report formula.
Lower Limit Displays the line of the defined lower limit value or report formula.
Font Defines the font for control chart labels.
Note: The Upper Limit, Target, and Lower Limit values or report formulas have to be defined on the Data Setting
properties page (5.4.4.1).
5.4.4.14 Appearance
This section allows a consistent color scheme for the objects in the interactive chart to be defined. The following items can
have their line color defined:
• Mean • 3s • Gridlines
• Linear trend line • Upper Limit • Minor Gridlines
• 1s • Target
• 2s • Lower Limit

Chromeleon 7

• Back Interior • Chart Interior

Border Style n.a. Defines the border style for the interactive chart:
None
Emboss
Arrangement Overlaid All charts are shown overlaid.
Stacked All charts are shown stacked (above each other).
3D Mode n.a. Shows chart as 3-dimensional chart.
5.4.4.15 SmartLink

Chromatogram overlays When selected, the injections that are overlaid in the
chromatogram plot for comparison define which injections are
displayed in the linked objects.
plot define which peaks are displayed in the interactive chart.
which peaks are shown in the interactive chart.
5.4.5 Contour/3D Plot

The Contour/3D Plot displays the 3D Field of a sample and associated data. When accessed from the layout presets the
view consists of a combination of four panes: - Peak Properties pane, Chromatogram plot, Spectra plot (or I-t plot for 3D
Amperometry) and the Contour/3D plot. The Peak Properties information pane cannot be modified by the display options
which are available for the other panes.
Figure 34 shows a typical Contour Plot layout corresponding to a preset pane configuration.
Figure 34: Contour Plot Panes Preset

The following Contour/3D plot options are available.

Chromeleon 7
5.4.5.1 Scale

Time Axis From: Defines the start value of the time axis.
To: Defines the end value of the time axis.
Autoscale When selected the contour plot and the chromatogram plot are
scaled to show the whole chromatogram. This option is also
available in the layout ribbon.
Units Minutes [min] or Seconds [s]
Scan Axis From: Defines the start value of the scan axis.
To: Defines the end value of the scan axis.
Autoscale When selected the contour plot and the spectra plot are scaled to
show the whole scan range. This option is also available in the
layout ribbon.
Signal Axis From: Defines the start value of the signal axis.
To: Defines the end value of the signal axis.
scaled to show the whole signal range.
Gradient Linear scale Signal values are colored using a linear scale.
Logarithmic scale Signal values are colored using a logarithmic scale. This option is
also available in the layout ribbon.
5.4.5.2 General

View 3D View Displays a three-dimensional view of the 3D data field from any
angle of view.
Data 3D data field If more than one type of 3D data field is available, the required field
can be selected from the list.
Axes Axis to Plot Gap Defines the distance in mm between the axes and the
chromatogram plot.
Font N/A Defines the font to be used for axes and labels in the Contour Plot.
Options Use black for zero Black represents a signal value of zero on the plot. This option
generates the fewest possible color repeats. A point’s color can
change when the scale changes.
Draw optimum integration path Draws the optimum integration path over the plot.
Spectra Retrieval Use raw spectra When selected raw spectra are shown and the UV settings from the
processing method are ignored. This option is also available in the
layout ribbon.
Apply baseline correction settings from When selected the settings selected on the UV Spectra tab page of
current processing method the processing method are applied to the raw data and include peak
spectrum bunching and baseline correction options. This option is
5.4.5.3 3D View Settings

Show Grid 3D View Shows a grid on the 3D plot.
Rotation X Type or select the angle of rotation around X axis of the 3D plot.
Y Type or select the angle of rotation around Y axis of the 3D plot.
Z Type or select the angle of rotation around Z axis of the 3D plot.
Reset Returns the axes to their default angles of rotation.
Performance N/A Best Quality using the same number of spectra used by the contour
plot. Best Performance using the fewest number of spectra.

Chromeleon 7
5.4.5.4 Title

Draw titles Shows a title for the contour/3D plot.
Font Allows the font for the contour/3D plot title to be defined.
7.2.
Chromeleon 7.2.
7.2.
toolbars on the plot axes are visible.
5.4.5.6 Contour/3D Plot Layout Ribbon

In addition, the following options are available in the layout ribbon.

Autoscale Full Size Resizes contour plot, chromatogram plot and spectra plot so that
the complete chromatogram and wavelength range are shown.
Time Resizes contour plot and chromatogram plot to show the full-time
scale.
Scan Resizes the contour plot and spectra plot to show the full scan
scale.
Color Gallery N/A Allows choosing from different color schemes for signal values in
the contour plot.
Overlays Stop Overlaying Scans Stops multiple scans being overlaid.
Optimum Integration Path Displays optimum integration path on the contour plot.
5.4.5.7 Chromatogram Plot

This Chromatogram plot pane of the Contour Plot layout preset offers the same functionality as the stand-alone
Chromatogram plot.
5.4.5.8 Spectra Plot Properties

This section defines the properties for the spectra plot pane of the Contour Plot layout preset. The following options are
available:
5.4.5.8.1 Frame & Axes

Axes Wavelength Axis Shows the wavelength axis.
Absorbance Axis Shows the absorbance axis.

Chromeleon 7

Font Allows defining the font to be used for the axes.
chromatogram plot.
Axis Titles Axis Titles Shows axis titles.
Units Shows units of the axis.
Font Allows defining the font to be used for the axis titles and units.
Grid Horizontal grid lines Applies horizontal grid lines to the spectra plot.
Vertical grid lines Applies vertical grid lines to the spectra plot.
Normalization None No normalization is performed. Signal response is reported in mAU.
Absolute maximum Performs spectra normalization relative to the absolute maximum of
the spectra.
Relative maximum Performs spectra normalization relative to the relative maximum of
the spectra.
Fixed Wavelength at Performs spectra normalization relative to the fixed wavelength
selected.
5.4.5.8.2 Label

Label Maxima Rotation Defines the angle the spectrum label is shown at.
Maxima count Defines how many maxima should be labeled.
Font Defines the font for the spectrum label.
Options Show match Displays the match of each spectrum with the corresponding main
spectrum. The main spectrum is either the peak spectrum, or a
reference spectrum (spectra comparison), or the top spectrum in a
spectra library selection.
Show baseline correction info Displays information about the baseline correction in the header.
Show overview plot When this check box is selected, the miniature overview of the calibration plot is
displayed when zooming into the calibration plot.
5.4.5.9 Export
The 3D field can be exported to a text file using the context menu command “Export 3DFIELD (text format)”. The command
launches a dialog with further options (Figure 35).
Figure 35: 3D Field Export Dialog Box


Chromeleon 7

Destination Clipboard Exports a textual description of the 3D data into the clipboard.
File Exports a textual description of the 3D data into a text file.
Additionally, the contour plot can be copied into the clipboard as an image using the Ctrl + C hotkey.
5.4.5.10 Extract
The extract command available from the context menu in the contour plot allows the user to extract information from the 3D
data.
5.4.5.10.1 Signals
This option allows a chromatogram measured at any wavelength to be extracted from the 3D data as a new chromatogram
file. The command launches a new dialog with further options (Figure 36).
Figure 36: Extract Signal Dialog Box with further options

Source 3D field Shows the 3D data field (read-only) from which the signals will be extracted.
Wavelength Wavelength of the chromatogram to be extracted
Use scan interpolation The resolution of a 3D field is, for example, 1.9 nm. Therefore, the data points are
usually not located at integer wavelengths. Select the Use scan interpolation check
box to calculate the chromatogram at the desired wavelength, via interpolation. If this
check is cleared, Chromeleon uses the chromatogram of the nearest wavelength.
Bandwidth Bandwidth to be used when extracting the chromatogram.
Result channel Channel name of the extracted file.
Unspiked.
5.4.5.10.2 Optimum Integration Path

A chromatogram that has been recorded at a fixed wavelength usually does not have an optimum Signal-to-Noise Ratio for
all included peaks. The selected wavelength is often a compromise that allows you to "see" all substances.
It would be ideal to detect peak 1 at 230 nm, peak 2 at 254 nm, peak 3 at 320 nm, etc.
This option extracts a chromatogram from the 3D field by selecting the wavelength for each peak that gives the optimum
signal-noise-ratio (Figure 37). Therefore, the wavelength changes throughout the chromatogram.

Chromeleon 7
Figure 37: Optimum Integration Path Dialog Box

Source 3D field Shows the 3D data field (read-only) from which the signals will be extracted.
Original channel Shows the name of the current (original) channel containing the 3D absorbance
data.
Bandwidth The bandwidth to be used when extracting the chromatogram.
Result channel Channel name of extracted file.
Unspiked.
5.4.5.10.3 Extract Amperometry Signals

This option allows a chromatogram at any waveform time to be extracted from the 3D Amp data set as a new chromatogram
file. The command launches a new dialog with further options.
Channel Name Channel name for the extracted file.
Extract Raw Data @ waveform time Extracts raw amperometric data corresponding to a single point along the waveform
axis
Extract integrated data Generates a chromatogram by integrating (summing) the signal points over the
specified integration interval (segment of the waveform). By default, only one
integration interval is listed; additional integration intervals can be defined by clicking
on the last row of the table and entering a retention time at which each new interval
should be applied, and the desired start times and end times of the integration
intervals (relative to the waveform cycle).
Use scan interpolation A 3D Amp data set may not have data points at the exact waveform time desired.
The Use scan interpolation check box calculates the chromatogram at the desired
waveform time, via interpolation. If this check box is cleared, Chromeleon uses the
chromatogram of the nearest waveform time.
Extract to all injections Extracts a chromatogram for each injection in the current sequence.
5.4.6 UV-Vis Spectra Pane

The spectra view can be modified to display peak spectra in various different ways. Figure 38 shows a typical UV-Vis
spectra view.

Chromeleon 7
Figure 38: UV-Vis Spectrum View

The following peak spectra display options are available.
5.4.6.1 Scale

Apply scaling to all plots N/A When linking is enabled and multiple spectral are displayed,
this option determines whether or not the scaling settings of
the currently selected plot apply to all linked plots.
Wavelength From Defines the start value of the wavelength axis.
To Defines the end value of the wavelength axis.
Autoscale When this is selected the plot is scaled to show the full
wavelength range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines the interval of tick
marks (the small lines that mark values) on the time axis. To
customize the intervals, select the Fixed intervals of tick marks
check box and then type or select a number in the Major tick
mark and/or Minor tick mark box. A tick mark interval of 0.0
removes the tick marks.
Absorbance From Defines the start value of the absorbance axis.
To Defines the end value of the absorbance axis.
absorbance range of the spectrum.

This section allows defining axes, grid and normalization of the spectral plot.

Axes Wavelength axis Displays a wavelength axis on the spectra plot.
Absorbance axis Displays an absorbance axis on the spectra plot.

Chromeleon 7

chromatogram plot.
Frame Displays a frame around the plot.
Axis Titles Axis Titles Applies titles to the spectra plot axes.
Units Displays units on the axes of the spectra plot.
Font Allows the font type and size of the axis titles to be defined
Orientation Horizontal Displays the plot in the landscape orientation.
Vertical Displays the plot in the portrait orientation.
Normalization None No normalization is performed. Signal response is reported in
mAU.
Absolute maximum Performs spectra normalization relative to the absolute
maximum of the spectra.
Relative maximum Performs spectra normalization relative to the relative
Fixed Wavelength at Performs spectra normalization relative to the fixed
wavelength selected.
5.4.6.3 Title

Draw titles Shows a title for the UV-Vis spectra plot.
Font Allows the font for the UV-Vis spectra plot title to be defined.
7.2.
Chromeleon 7.2.
7.2.
5.4.6.4 Peak Spectra

This section allows selecting which spectra should be shown.

Spectra Sampling Points Apex Spectrum Displays the spectrum at the peak apex.
Front 1 (%) Displays the spectrum at the selected % height of the peak
ascending flank.
ascending flank.
Tail 1 (%) Displays the spectrum at the selected % height of the peak
tailing flank.

Chromeleon 7

tailing flank.
Reference Spectrum None No reference overly is displayed.
Apex spectrum of recent The spectrum of the currently displayed peak is overlaid with
calibration standard the spectrum of the peak with the same name from the last
calibration standard injection of the sequence.
Apex spectrum of a fixed injection The spectrum of the currently displayed peak is overlaid with
the spectrum of the peak with the same name from the
selected injection.
Reference spectrum in The spectrum of the currently displayed peak is overlaid with
corresponding component table the reference spectrum from the component table of the
processing method.
Spectral library screening results The spectrum of the currently displayed peak is overlaid with
the spectra of the results of the spectral library screening (the
number of hits to be shown can be selected).
5.4.6.5 Label
This section allows defining how labels are shown in the spectral plot.

Maxima count Defines how many maxima should be labeled.
Options Show match factor Displays the match of each spectrum with the corresponding
main spectrum. The main spectrum is either the peak
spectrum, or a reference spectrum (spectra comparison), or
the top spectrum in a spectra library selection.
Show baseline correction info Displays information about the baseline correction in the
header.
5.4.6.6 Analysis
This section controls how spectra analysis is performed.

Spectra Analysis None No analysis is performed.
Difference Forms the difference between the main spectrum and the
remaining individual spectra of the pane. Depending on
whether normalization is performed (see Frame & Axes),
representation of the difference spectra is in percent or in the
corresponding dimension; for example, mAU.
First derivative Calculates and displays the first derivative of each spectrum
displayed.
Second derivative Calculates and displays the second derivative of each
spectrum displayed.
Background spectra used for Displays the subtracted background spectrum in a separate
baseline correction spectra plot.
Overlay Overlay background spectra used Overlays the spectrum with the spectrum used for baseline
for baseline correction correction.
Overlay spectra without baseline Overlays each spectrum with the corresponding spectrum
correction without baseline correction.
5.4.6.7 Comparison
This section defines comparing multiple spectral. The following options are available:

Arrangement Overlaid All overlaid plots are shown in one window.

Chromeleon 7

Stacked All overlaid plots are shown in stacked windows.
Offset Scan Offset Offsets the overlaid plots by the % scan value selected.
Intensity Offset Offsets the overlaid plots by the % intensity value selected.
Overlay Overlay with right signal axis. If selected the overlaid plot is measured against a right signal
axis.
Mirror Mirror signal Inverts the intensity axis of the overlaid or stacked plots.

This section allows the color of each item in the peak spectra plot to be defined. The following items can have their color
defined:
• Grid lines • Uncorrected spectrum • First front spectrum
• Axes • Spectrum 1-8 • Second front spectrum
• Reference Spectrum • Library Spectrum 1-7 • First tail spectrum
• Background spectrum • Apex Spectrum • Second tail spectrum
• Background
5.4.6.9 SmartLink
5.4.6.9.1 Link to Chromatogram

5.4.6.9.2 Link to Injection

Link to Injections Allows multiple injections to be included in the array of Sm
Include Current Selections/Pins In addition to those injections specified by type or by c
(below), the currently selected and pinned injections w
the list of SmartLink injections
Custom Conditions Only include injections that match Displays only injections that fulfill certain conditions,
the following conditions variables.

Chromeleon 7

Link to Injections Allows multiple injections to be included in the arra
Include Current Selections/Pins In addition to those injections specified by type
(below), the currently selected and pinned inject
ALL (Any field from the injection Restrict the data points shown based on comparin
list – including user defined with a user-defined value and using the following l
columns) Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
AND [Any field from the injection As for the previous parameter.
columns]
or Allows for matching based on only one compariso
and Forces matching based on every rule in the list.
overrides the requirement to match every compar
list.
5.4.6.9.3 Display By
Defines how the SmartLink objects will be ordered.
Peaks per injection When a single injection is selected, the peak objects for that injection are plotted in horizontal order.
When multiple injections are selected, each injection has its own row and each peak has its own column.
Injections per peak When a single peak is selected, the peak objects for each injection are plotted in horizontal order.
When multiple peaks are selected, each peak has its own row and each injection has its own column.

Show overview plot When this check box is selected, the miniature overview of the plot is displayed
when zooming into the plot.
toolbars on the plots axes are visible.
5.4.6.11 Spectra Plot Tools Contextual Ribbon

In addition, the following options are available in the Spectra Plot Tools Contextual ribbon:

Chromeleon 7

Autoscale Full Size Resizes spectra plot so that the full response and wavelength range
are shown.
Wavelength Resizes spectra plot so that the full wavelength range is shown.
Absorbance Resizes spectra plot so that the full response range is shown.
Library Find in Library Performs a library search in any spectra library available in the
sequence and shows the results in the “Ad Hoc Library Search”
window.
Add Spectrum Adds the currently visible spectrum to the library selected in the
library selection drop list.
Add All Spectra Adds all retention spectra in this chromatogram to the library
selected in the library selection drop list.
N/A (list of spectral libraries in the Selects the library where spectra should be added.
sequence)
Previous peak Selects the previous peak.
Next peak Selects the next peak.
5.4.6.12 Ad Hoc Library Search Window

This window (
Figure 39) shows the results of a library search initiated from the layout ribbon of the spectra plot.
On the upper left criteria for the library search can be defined; on the upper right the currently selected spectrum overlaid
with any selected library spectrum is shown.
On the lower half a list of all library matches according to the defined criteria is shown. Spectra can be selected by clicking in
the list holding down Shift or Ctrl keys.
Figure 39: Ad Hoc Library Search Window

The following search criteria are available in the Ad Hoc Library Search window:

Spectral Libraries to be N/A (list of all libraries in the sequence) Each library with a set check mark is included in the search.
searched in It is also possible to specify that all libraries in a given folder will be
searched.

Chromeleon 7

Spectral Match Conditions Match Criterion Determines the mathematical method that is used for comparing
spectra.
Least Square: Forms the sum of the squared signal deviations at
each wavelength and determines the average square deviation
between two spectra (standard method).
Weighted Least Square: The squared deviations are weighted by the
signal height (for spectra extracted close to the detection limit).
Correlation: Usual match criterion in statistics if a linear correlation
between two curves is presumed (similar to Least Square; usually
provides the same result).
Hit Threshold Hits below the specified Match Factor are not returned.
Spectrum Derivative Specifies if library screening is to be performed based on a derivative
of the peak spectrum.
None: Disables library screening based on a derivative of the peak
spectrum.
1st Derivative: Calculates and displays the first derivative of each
spectrum plot displayed. This type of representation increases
absorption or current maxima and thus enables a better evaluation of
whether two spectra plots are from the same substance or not.
2nd Derivative: Calculates and displays the second derivative of
each spectrum plot displayed. The "exaggeration" of local maxima is
further increased.
Restrict Wavelength Range from Restricts the wavelength range for spectra screening.
5.4.6.13 Export
The spectrum can be exported to a text file using the context menu command “Export Spectrum (text format)”. The
command launches a dialog with further options (Figure 40).
Figure 40: Spectrum Export Dialog Box


Destination Clipboard Exports a textual description of the spectrum data into the
clipboard.
File Exports a textual description of the spectrum data into a text
file.
Options Format Export format: CM-ASCII or STIP-ASCII.
Parameters Options to use baseline correction settings from Processing
Method or use fixed scan step.
Additionally, the spectrum plot can be copied into the clipboard as an image using the Ctrl + C hotkey.

Chromeleon 7
5.4.7 Fluorescence Spectra Pane

The fluorescence spectra pane can be modified to display excitation and emission spectra in various ways. Figure 41 shows
a typical fluorescence spectra view.
Figure 41: Fluorescence Spectra Pane

The following peak spectra display options are available.
5.4.7.1 Scale

Intensity From Defines the start value of the intensity axis.
To Defines the end value of the intensity axis.
intensity range of the spectrum.

This section allows defining axes, grid and normalization of the fluorescence spectral plot.

Chromeleon 7

Intensity axis Displays an intensity axis on the spectra plot.
chromatogram plot.
mAU.
Absolute Maximum Performs spectra normalization relative to the absolute
Relative Maximum Performs spectra normalization relative to the relative
Fixed Wavelength at Performs spectra normalization relative to the fixed
wavelength selected.
5.4.7.3 Title

Draw titles Shows a title for the fluorescence spectra plot.
Font Allows the font for the fluorescence spectra plot title to be
defined.
7.2.
Chromeleon 7.2.
7.2.
5.4.7.4 Spectra Filter

This section allows defining which fluorescence spectra are shown.

Scan type Any Displays any spectrum found, regardless of the scan type.
Emission Displays emission scans only.
Excitation Displays excitation scans only.
Synchronous Displays synchronous scans only.

Chromeleon 7

Photomultiplier Any Displays any spectrum found, regardless of which
photomultiplier tube (PMT) measured the spectrum.
Photomultiplier 1 Displays spectra measured by the primary PMT only.
Photomultiplier 2 Displays spectra measured by the secondary PMT only.
More Options N/A Adds additional filter criteria.
5.4.7.5 Overlay
This section allows reference spectra overlays.

Reference Overlay None Displays only the fluorescence spectra of the selected peak.
Peak Spectra of recent calibration Overlays the fluorescence spectra from a matching peak from
standard the most recent available standard (backwards in time).
Peak Spectra of a fixed injection Overlays the fluorescence spectra from a matching peak from
a manually selected injection.
5.4.7.6 Label

Maxima Count Defines how many maxima should be labeled.
Options Show match Displays the match of each spectrum with the corresponding
header.
5.4.7.7 Analysis

Difference Forms plots representing the difference between the main
spectrum and the remaining individual spectra of the pane.
Depending on whether normalization is performed (see Frame
& Axes), representation of the difference spectra is in percent
or in the corresponding dimension.
displayed.
spectrum displayed.
5.4.7.8 Comparison


Chromeleon 7

axis.

defined:
• Grid lines • Uncorrected spectrum • Second front spectrum
• Axes • Spectrum 1-8 • First tail spectrum
• Reference spectrum • Apex Spectrum • Second tail spectrum
• Background spectrum • First front spectrum
• Background
5.4.7.10 SmartLink


Link to Injections Allows multiple injections to be included in the array of SmartLink objects
Include Current Selections/Pins In addition to those injections specified by type or by custom condition
(below), the currently selected and pinned injections will be included in
Custom Conditions Only include injections that match Displays only injections that fulfill certain conditions, based on report

Chromeleon 7

ALL (Any field from the injection Restrict the data points shown based on comparing the selected variable
list – including user defined with a user-defined value and using the following logical arguments:
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
or Allows for matching based on only one comparison in the rule
and Forces matching based on every rule in the list. The or sub parameter
overrides the requirement to match every comparison in the specific rule
list.

toolbars on the plots axes are visible.
5.4.7.12 Spectra Plot Tools Layout Ribbon

In addition, the following options are available in the layout ribbon:

Chromeleon 7

Autoscale Full Size Resizes spectra plot so that the full response and wavelength range
are shown.
Wavelength Resizes spectra plot so that the full wavelength range is shown.
Intensity Resizes spectra plot so that the full intensity range is shown.
5.4.8 I-t Plot Pane

The I-t Plot pane displays plots of current versus waveform time when a selected injection has 3D amperometric data.
These I-t plots may be “Peak I-t Plots”, which are retrieved from the chromatographic peak currently selected in the
Chromatogram pane at up to 5 pre-defined points of the peak, and/or “Time I-t Plots” that correspond to manually selected
points along the chromatogram.
Figure 42 shows a typical I-t plot pane display.
Figure 42: I-t Plot Pane
The following display options are available for Peak I-t Plots.
5.4.8.1 Scale

Waveform Time From Defines the start value of the waveform axis.
To Defines the end value of the waveform axis.
Autoscale When this is selected, the plot is scaled to show the full
waveform range of the I-t plot.

Chromeleon 7

Current From Defines the start value of the response axis.
response range of the I-t plot.

This section defines settings for the axes, grid and normalization of the I-t plot.

Axes Waveform time axis Displays a waveform time axis on the I-t plot.
Current axis Displays a current axis on the I-t plot.
chromatogram plot.
Axis Titles Axis Titles Applies titles to the I-t plot axes.
Units Displays units on the axes of the I-t plot.
Grid Horizontal grid lines Applies horizontal grid lines to the I-t plot.
Vertical grid lines Applies vertical grid lines to the I-t plot.
mAU.
Absolute Maximum Performs I-t plot normalization relative to the absolute
maximum of the I-t plots.
Relative Maximum Performs I-t plot normalization relative to the relative
Fixed Waveform Time at Performs I-t plot normalization relative to the fixed waveform
time point selected.
5.4.8.3 Title

Draw titles Shows a title for the I-t plot.
Font Allows the font for the I-t plot title to be defined.
7.2.

Chromeleon 7

Chromeleon 7.2.
7.2.
5.4.8.4 Peak I-t Plots

This section defines which I-t plots are shown.

I-t plot Sampling Points Apex I-t plot Displays the I-t plot at the peak apex.
Front 1 (%) Displays the I-t plot at the selected % height of the peak
ascending flank.
ascending flank.
Tail 1 (%) Displays the I-t plot at the selected % height of the peak tailing
flank.
flank.
Reference Overlay None No reference overlay is displayed.
Apex I-t plot of recent calibration The I-t plot of the currently displayed peak is overlaid with the I-
standard t plot of the peak with the same name from the last calibration
standard injection of the sequence.
Apex I-t plot of a fixed injection The I-t plot of the currently displayed peak is overlaid with the I-
t plot of the peak with the same name from the selected
injection.
5.4.8.5 Label
This section defines how labels are shown in the I-t plot.

Label Maxima Rotation Defines the angle at which the I-t plot label is shown.
Font Defines the font for the I-t plot label.
Options Show match factor Displays, in the caption for each I-t plot, the match factor for
that I-t plot relative to the corresponding main I-t plot. The main
I-t plot is either the peak I-t plot, or a reference I-t plot (I-t plot
comparison).
Show baseline correction info Displays information about baseline correction in the caption of
each I-t plot.
5.4.8.6 Analysis
This section controls how I-t plot analysis is performed.

I-t plot Analysis None No analysis is performed.
Difference Forms the difference between the main I-t plot and the
remaining individual I-t plots of the pane. Depending on
representation of the difference I-t plots is in percent or in the
corresponding dimension (nA).

Chromeleon 7

First derivative Calculates and displays the first derivative of each I-t plot
displayed.
Second derivative Calculates and displays the second derivative of each I-t plot
displayed.
5.4.8.7 Comparison

axis.

This section defines the color of each item in the peak I-t plot. The following items can have their color defined:
• Grid Lines • Uncorrected I-t plot • Second Front I-t plot
• Axes • I-t plot 1-8 • First Tail I-t plot
• Reference I-t plot • Apex I-t plot • Second Tail I-t plot
• Background I-t plot • First Front I-t plot
• Background
5.4.8.9 SmartLink


toolbars on the plot’s axes are visible.
5.4.8.11 I-t plot Layout Ribbon

In addition to the above settings, which are all available via the Properties dialog of the I-t Plot Pane, the following options
are available in the layout ribbon:

Chromeleon 7

Autoscale Full Size Resizes I-t plot so that the full response and waveform range are
shown.
Waveform Time Resizes I-t plot so that the full waveform range is shown.
Current Resizes I-t plot so that the full current range is shown.
5.4.8.12 Export
The I-t plot can be exported to a text file using the context menu command “Export Spectrum (Text format)”. The command
launches a dialog with further options (Figure 43).
Figure 43: Spectrum Export Dialog Box


Destination Clipboard Exports a textual description of the spectrum data into the
clipboard.
File Exports a textual description of the spectrum data into a text
file.
Options Format Export format: CM-ASCII or STIP-ASCII.
Parameters Options to use baseline correction settings from Processing
Method or use fixed scan step.
Additionally, the I-t plot can be copied into the clipboard as an image using the Ctrl + C hotkey.
5.4.9 Interactive Results Pane

The interactive results tables contain a set of report tables that provide a screen view of the chromatographic data. Each
specific report table has its own specific data and can be customized as required.
The report tables that can be included are the same as the report tables in the Report Template (except the Fraction and
Tube Report tables):
• Results Table: Integration (see section 5.7.20.2)
• Results Table: Peak Summary (see section 5.7.20.3)
• Results Table: Consolidated Table (see section 5.7.20.4)
• Results Table: Test Case (see section 5.7.20.5)
• Results Table: MS Raw Spectra (see section 5.7.20.6)
• Results Table: Frame Table (see section 5.7.20.7)
• Results Table: Tentative Identification (see section 5.7.20.8)
• Processing Method Table: Component Table (see section 5.7.20.10)
• Processing Method Table: Peak Group Table (see section 5.7.20.13)

Chromeleon 7
• Processing Method Table: Detection Settings (see section 5.7.20.14)

• Processing Method Table: Calibration History (see section 5.7.20.15)
• Processing Method Table: System Suitability IRC (see section 5.7.20.16)
• Processing Method Table: MS Detection Settings (see section 5.7.20.17)
• Processing Method Table: Peptide Table (see section 5.7.20.18)
• Instrument Method Table: Overview (see section 5.7.20.19)
• Instrument Method Table: Script (see section 5.7.20.20)
• Instrument Method Table: MS Instrument Method (XRAW) (see section 5.7.20.21)
• Instrument Method Table: MS Tune (see section 5.7.20.22)
• Instrument Method Table: Smart Startup/Shutdown/Standby Settings (see section 5.7.20.23)
• Instrument Method Table: Extended (see section 5.7.20.24)
• Status and Audit Table: Audit Trail (see section 5.7.20.25)
• Status and Audit Table: Data Audit Trail (see section 5.7.20.26)
• Status and Audit Table: Chromeleon 6 History (see section 5.7.20.26)
• Status and Audit Table: MS Device Information (see section 5.7.20.27)
• Status and Audit Table: MS Status Log (see section 5.7.20.29)
• Fractionation Table: Fraction Report (see section 5.7.20.30)
• Fractionation Table: Tube Report (see section 5.7.20.31)
Additionally, for the tables that support this, the grouping options apply (see section 5.7.20.1).
5.4.10 Injection Rack Pane

The injection rack pane provides a graphical display of the injection vial positions for the current sequence in the assigned
instruments autosampler. The following options are available:
In the Injection Rack pane properties dialog, there are several options:
5.4.10.1 General
view.
zoom allows.)
supported.
5.4.10.2 Title
Draw Title N/A Displays the title in the top center of the plot.

Chromeleon 7
Font N/A Allows defining the font to be used for the title of the plot.
5.4.10.3 Tooltip
Enable tooltip Displays information about a vial/tube.
Tooltip formula The content of the tooltip can be adapted depending on the context the Rack View
control is used, based on variables contained in the Injection category section 7. X.
Scaling Enable scaling Disables zooming of the rack view.
Rotation Enable rotation Disables rotation of the rack view.
5.4.11 Fraction Tray Pane

The fraction tray pane provides a graphical display of the fraction tube positions for the current sequence in the assigned
In the Fraction Tray pane properties dialog, there are several options:
5.4.11.1 General
view.
zoom allows.)
5.4.11.2 Title
5.4.11.3 Fill styles

In the fraction tray, the fill colors of various objects can be defined. The following options are available:
Tubes collected during sequence run N/A Defines the color for all tubes collected during the current sequence
Tubes collected from current injection N/A Defines the color for all tubes from the currently selected injection
Currently selected tube/fraction N/A Defines the color of the currently selected tube or fraction
5.4.11.4 Tooltip

Chromeleon 7
Tooltip formula The content of the tooltip can be adapted depending on the context the Tray View
5.4.12 Mass Spectrum Pane

The Mass Spectrum view allows the user to graphically view and interact with the mass spectrum plot(s) extracted from the
sample data. Figure 44 shows a typical mass spectrum view:
Figure 44: Mass Spectrum View in Chromatography Studio
5.4.12.1 Zooming and Navigating in the Mass Spectrum

The mass spectrum view allows zooming and navigating as required with the following options:
Undo Zoom Reverts the recent zoom operation and returns to the previous view. Accessed by
right-clicking on the plot and selecting Unzoom
Full Scale Reverts the recent all zooming and re-plots the data full scale. Accessed by right-
clicking on the plot and selecting Full Scale

Chromeleon 7
Y axis zoom tools Shown when moving the cursor over the Y axis. The following functions are
available:
+ zooms into the plot vertically
Autoscale Signal resizes the plot height to the highest mass abundance currently
visible
- zooms out of the plot vertically
X axis zoom tools Shown when moving the cursor over the X axis. The following functions are
available:
+ zooms into the plot horizontally
Autoscale Time resizes the plot to the complete mass range of the acquired data.
- zooms out of the plot horizontally
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click the full-
size button to autoscale both axes simultaneously.
Double Click on the abundance axis Automatically resizes the plot height to the highest mass abundance currently
visible.
Double Click on the m/z axis Automatically resizes the plot width to the complete mass pane of the acquired data
Drag the abundance axis Scrolls the y axis limits
Drag the m/z axis Scrolls the x axis limits
5.4.12.2 Copy
Copies the mass spectrum plot to the clipboard as an image. This is also possible by using the Ctrl + C hotkey.
5.4.12.3 Zero Mass Offset

The zero-mass offset feature lets you set any mass on the mass spectral plot as the zero mass point. The masses of all
mass peaks on the plot are then shown relative to the new zero point. To use, point to the mass on the mass spectral plot
that you want to set as the new zero point, and select this context menu item.
5.4.12.4 Remove Zero Mass Offset

Removes any previously set zero mass offset for the plot.
5.4.12.5 Extract Ion Chromatogram

The function allows the user to extract ion chromatograms from the data set. Selecting this context menu item displays the
following dialog:

Chromeleon 7
Figure 45: Extract Mass Spectrum Channel
Trace Specify the chromatogram trace type to be extracted
TIC (Total Ion Current)—all ions matching the filter entered in the Filter list will be extracted from the
raw data.
Base Peak—base peak ions that match the filter entered in the Filter list will be extracted from the
raw data.
Mass Range—ions that match the filter entered in the Filter list and with a mass that matches the
mass or mass range entered in the Mass range(s) box will be extracted from the raw data.
Filter Specifies the acquisition filter from which the chromatogram will be extracted
Mass ranges Defines the mass, mass range, or a set of mass ranges to be extracted
Smoothing Specifies the type of smoothing to be performed on the chromatogram data when it is extracted.
Channel Name Defines the label that will be used to identify this extracted ion chromatogram in the channels list
Make channel permanent Creates a permanent channel when selected or if check box is clear a temporary channel is
created.
5.4.12.6 Clear Temporary Extract Ion Chromatograms

Removes any temporary ion chromatograms previously extracted from the data
5.4.12.7 Export Spectrum

Exports the mass spectrum to a text file. The following options are available:

Destination Clipboard Exports a textual description of the mass spectrum data into
the clipboard.
File Exports a textual description of the mass spectrum data into a
text file.
Format CM-ASCII The exported mass spectrum contains complete information
STIP-ASCII The exported mass spectrum plot contains condensed
information
Parameters Use baseline correction settings Uses the baseline correction settings from MS settings tab of
from Processing method the processing method
Use fixed scan step Changes the resolution for the exported mass spectrum
5.4.12.8 Remove Time Spectra

Removes any time spectra plots sharing the pane with the peak spectrum

Chromeleon 7
5.4.12.9 Find in Library

This menu item performs an ad hoc library search on the displayed mass spectrum using the parameters specified on the
MS Library Search tab of the processing method.
The following search window is displayed:
Figure 46: Ad Hoc Library Search Window

In the top section, criteria for the library search can be defined. In the middle section, search results are displayed. In the
bottom section, the reference and library spectra are displayed.
The following search criteria are available in the Ad Hoc Library Search window:

MS Libraries to be N/A (list of all libraries in the sequence) Each library with a set check mark is included in the search.
searched in
Normal: Uses a standard pre-screen search filter. This is the default
search type.
Penalize Rare Compounds: Limits the impact of rare compounds by
reducing their match factors. This option is effective only when you
have selected a NIST Mass Spectral Library (such as, mainlib). It
has no effect on spectra in internal NIST libraries or other
commercial libraries.
Each reference spectrum in a NIST Mass Spectral Library contains a
record of other commercial libraries containing information about the
compound. A compound is considered 'rare' if it is present in a
limited number of these libraries.

Chromeleon 7

Similarity Simple: Finds a large set of spectra to compare with the submitted
spectrum. This search option is generally slower than an identity
search.
Hybrid: Uses a combination of the Simple and Neutral Loss search
types. When Hybrid is selected, the Search with Mol. Weight edit box
under Search Options is enabled. Enter an estimate of the submitted
spectrum's molecular weight.
Neutral Loss: Compares neutral losses of the submitted spectrum
with spectra in the library data. The neutral losses in a spectrum are
the mass differences between the molecular ion and other major
ions in the spectrum. For certain classes of compounds, neutral
losses can be a very characteristic spectral feature. In a Neutral Loss
search, Chromeleon identifies the molecular ion of the submitted
spectrum and includes the molecular ion in the search, along with
the spectrum. Significant neutral losses of the submitted spectrum
are calculated and compared with the library data. Hits are returned
according to matches of the molecular ion and its neutral losses.
When Neutral Loss is selected, the Search with Mol. Weight edit box
under Search Options is enabled. Enter an estimate of the submitted
spectrum's molecular
Search with Molecular Wt When a value is supplied, searches will be restricted to library entries
with the indicated molecular weight.
Reverse Search When checked, this parameter indicates that a reverse search will be
performed instead of a standard search
Thresholds Match Factor Defines the minimum match factor below which matches will not be
reported
Reverse Match Factor Defines the minimum reverse match factor below which matches will
not be reported
Probability Defines the minimum probably below which matches will not be
reported
The following sections describe the tabs of the Properties dialog accessed from the context menu.
5.4.12.10 Scale

Apply scaling to all plots N/A Allows the user to apply the same scaling to all plots
simultaneously when checked.
Mass From Defines the start value of the mass axis.
To Defines the end value of the mass axis.
Autoscale When this is selected the plot is scaled to show the full mass
range of the data
intensity range of the mass spectrum.

Chromeleon 7

This section allows defining axes, grid and normalization of the mass spec plot.

Axes Mass axis Displays a mass axis on the mass spec plot.
Intensity axis Displays an abundance axis on the mass spec plot.
Axis to Plot Gap Defines the distance in mm between the axes and the plot.
Frame Displays a frame around the plot
Axis Titles Axis Titles Applies titles to the mass spec plot axes.
Units Displays units on the axes of the mass spec plot.
Grid Horizontal grid lines Applies horizontal grid lines to the mass spec plot.
Vertical grid lines Applies vertical grid lines to the mass spec plot.
Orientation Horizontal Scan type is the horizontal axis, and signal is the vertical axis
Vertical Scan type is the vertical axis, and signal is the horizontal axis.
Normalization None No normalization is performed.
5.4.12.12 Title

defined.
7.2.
Chromeleon 7.2.
7.2.

This section allows selecting which auxiliary mass spectra should be shown.

Spectra Sampling Points Apex Spectrum Displays the mass spectrum at the peak apex as a thumbnail
Front 1 (%) Displays the mass spectrum at the selected % height of the
peak ascending flank as a thumbnail.

Chromeleon 7

Tail 1 (%) Displays the mass spectrum at the selected % height of the
peak tailing flank as a thumbnail.
Apex spectrum of recent The mass spectrum of the currently displayed peak is overlaid
calibration standard with the mass spectrum of the peak with the same name from
the last calibration standard injection of the sequence.
Apex spectrum of a fixed injection The mass spectrum of the currently displayed peak is overlaid
with the mass spectrum of the peak with the same name from
the selected injection.
Spectral library screening results The mass spectrum of the currently displayed peak is overlaid
with the mass spectra of the results of the spectral library
screening (the number of hits to be shown can be selected).
5.4.12.14 Label
This section allows defining how labels are shown in the mass spectral plot.

Peak Label Rotation Defines the angle the mass spectrum label is shown at.
Maximum threshold The threshold intensity (in %) at which mass peaks will be
labeled
Font Defines the font for the mass spectrum label.
Options Show baseline correction info Displays information about the baseline correction in the
header.
Show detected mass info for peak Checking this box will cause the detected mass for the peak
spectra spectrum to be displayed horizontally on top of the mass peak.
If the monitored mass is not detected, no information is
displayed.
Show detected mass info for time Checking this box will cause the detected mass for the time
displayed.
5.4.12.15 Analysis
This section controls how mass spectra analysis is performed.

Difference Forms the difference between the main mass spectrum and
the remaining individual mass spectra of the pane. Depending
on whether normalization is performed (see Frame & Axes),
representation of the difference mass spectra is in percent or
in the corresponding dimension;
Overlay Overlay background spectra used Overlays the mass spectrum with the mass spectrum used for
for baseline correction baseline correction.
Overlay spectra without baseline Overlays each mass spectrum with the corresponding mass
correction spectrum without baseline correction.
5.4.12.16 Comparison
This section allows defining how multiple mass spectra are arranged

Arrangement Stacked Plots are stacked on a single plot and share the same scan axis;
each stacked plot has a separate intensity axis.

Chromeleon 7

Overlaid Plots are overlaid on a single plot and share the same scan and
intensity axes
Offset Scan Offset To offset overlaid plots on the scan axis, select the check box and
enter the offset percentage in the box.
Intensity Offset To offset overlaid plots on the intensity axis, select the check box
and enter the offset percentage in the box
Overlay Overlay with right signal axis When plots are overlaid, select this check box to include a second
signal axis on the right side of the plot
Mirror Mirror Signal Select this check box to invert the intensity axis of the overlaid or
stacked plots. The plots "mirror" the main spectrum or I-t plot.

This section allows the color of each item in the mass spec plot to be defined. The following items can have their color
defined:
• Axes • Spectrum 1-8 • First Tail spectrum
• Background
5.4.12.18 MS Settings

TIC Spectrum Filter Filter This option works in combination with the Time Spectra Tool to
select a mass spectrum from a specific acquisition filter.
Select the acquisition filter in the Filter list (or type a filter definition),
and then use the Time Spectra Tool to select a retention time on the
chromatogram. The spectrum from the selected filter at the selected
retention time is shown on the plot.
If the selected filter was not in use at the selected retention time, the
spectrum at the retention time nearest to when the selected filter was
in effect is shown.
Noise Reduction Use setting of processing method Use the parameters from the MS Settings page of the processing
method.
Do not reduce Noise No noise reduction calculations will be performed
Relative Threshold Allows masses below a specified percentage of the base peak to be
ignored
5.4.12.19 Data Presentation

Plot Mode Automatic Select this option to display the mass spectral data in the format in
which it was acquired. For centroid format data, the plot displays a
discrete vertical line for each mass peak. For profile format data, the
plot is a continuous curve, with each mass peak consisting of
multiple data points.
Centroid Select this option to always display the data in centroid format, even
if profile data was acquired.
Mass precision N/A Select whether to use the mass precision defined on the MS
Settings tab page of the processing method, or to define a custom
number of significant figures to include in the mass peak labels on
the plot.

Chromeleon 7

Mass tolerance N/A Select whether to use the default mass tolerance range defined on
the MS Settings page of the processing method, or to define a
custom range.
5.4.12.20 SmartLink
This section defines how the SmartLink functionality applies to the mass spec plot
5.4.12.20.1Link to Chromatogram

Link to Chromatogram N/A When this option is selected, the plot will adapt to show only the
spectra for peaks visible in the chromatogram plot. When the plot
is linked, the plot pane splits into several panes to show plots from
multiple peaks
plot define which peaks are displayed in the mass spec plot
which peaks are shown in the mass spec plot
5.4.12.20.2Link to Injection


Chromeleon 7

Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
list.
5.4.12.20.3Display By

This section defines what optional zoom/unzoom tools are displayed on the mass spec plot
Show overview plot When this check box is selected, the miniature overview of the mass spectrum plot

Chromeleon 7
5.4.13 MS Components Pane

The MS Components pane allows the user to visualize and interact with MS component quantitation and confirmation (if
applicable) XICs.
Figure 47: MS Components View in Chromatography Studio
5.4.13.1 Zooming and Navigating in the MS Components View

The MS Components view allows zooming and navigating as required with the following options:
available:
Autoscale Signal resizes the plot height to the data point with the highest intensity
currently visible
available:
Autoscale Time resizes the plot to the complete time range of the XIC as defined by

Chromeleon 7
Double Click on the intensity axis Automatically resizes the plot height to the highest intensity data point currently
visible.
Double Click on the time axis Automatically resizes the plot width to the complete time range of the XIC as
defined by the processing method.
5.4.13.2 Copy
Copies the MS Components plot to the clipboard as an image. This is also possible using the Ctrl + C hotkey.

Exports the MS Components plot to a text file. When 1 or more confirmation XICs are displayed, the exported data is for the
plot where the context menu was activated. The following options are available:

Destination Clipboard Exports a textual description of the MS component trace into
the clipboard.
File Exports a textual description of the MS component trace into a
user defined text file.
Options Chromatogram data The exported MS component trace includes any corrections
such as a delay time or chromatogram subtraction.
Raw data The exported MS component trace is the raw data as
acquired without corrections
5.4.13.4 Tools
Automatic Tool The tools in this section are selected either automatically when the “Automatic” tool
is active based on the cursor position
Delimiter Tool Used to move the peak start or peak end.
Baseline Tool Used to modify the baseline.
Peak Window Tool Used to modify peak detection window
Detection Parameter Tool User to move or edit detection parameters
Insert Peak Tool Used to create a new peak.
Spectra Plot Tool Used to display mass spectrum of selected data point.
Zoom Tool Used to zoom into MS component plot
5.4.13.5 Insert Detection Parameter…

When Chromeleon 6 or Cobra algorithms are selected in the MS Detection tab in the processing method, Insert Detection
Parameters… becomes enabled. This allows the user to insert additional detection parameters at the retention time of the
cursor
5.4.13.6 Edit Detection Parameter…

If detection parameters are available in the MS component trace window, right clicking on a parameter and selecting Edit
Detection Parameter… allows the user to modify the selected Chromeleon 6 or Cobra detection parameter
5.4.13.7 Delete Detection Parameter(s)

If detection parameters are available in the MS component trace window, right clicking on a parameter and selecting Delete
Detection Parameter(s) allows the user to delete the selected Chromeleon 6 or Cobra detection parameter.

Chromeleon 7
5.4.13.8 Show Spectrum

Similar to the Time Spectra Tool in the Chromatogram pane Layout ribbon, this allows the user to display the mass
spectrum of the data point nearest the mouse cursor.
5.4.13.9 Overlay Spectrum

This allows the user to add additional spectra to the MS Spectra pane. If the MS Spectrum layout is set to Overlaid, the new
spectrum will be overlaid. Otherwise, the new spectrum will be displayed stacked.
5.4.13.10 Remove Time Spectra

This removes all mass spectra that were displayed using the Show Spectrum and Overlay Spectrum functions
5.4.13.11 MS Spectra Baseline Correction
No Baseline Correction Mass spectra display functions are forced to display uncorrected spectra
Peak Dependent Correction Mass spectra display functions are forced to display spectra adjusted for bunching
regions before and after the end of the selected peak as defined by the processing
method
Fixed Correction Mass spectra display functions are forced to display spectra adjusted for an explicit
baseline region defined by a start and end time in the processing method.
5.4.13.12 Properties
The following MS Component display options are available:
5.4.13.12.1Plot Details
This section defines which parts of the plot framework are shown. The parameters available are:

chromatogram plot.
5.4.13.12.2Time Axis
The time window for MS Component plots is defined in the component table of the processing method and cannot be
changed on this page. Separate time axes and tick mark intervals are not supported for MS Components. Please refer to
section 5.3.2.20 for more details.
5.4.13.12.3Signal Axis

Range for component XICs Autoscale or Fixed Determines the method for selecting the range. Can be set to:

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Autoscale using reference Autoscale or Fixed, Autoscale using reference injection or Fixed
injection using Formula.
Fixed using formula

Fixed using Formula From Defines the start value of the signal axis using a report variable
formula
To Defines the end value of the signal axis using a report variable
formula
5.4.13.12.4Title
selected either based on simple text values or on user-defined formulas. The formula can be based on variables from the
following sections:
• General (7.2)
• Sequence (7.3)
• Injection (0)

Legend Draw legend Displays the user-defined legend string in a legend box on the
MS Component plot.
5.4.13.12.5Peak Characterization
This section defines how detailed peaks are characterized in the MS Components plot. The following options are available:


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main peak.
rider peak.
Peak widths Shows peak widths.
Draw peak width at Draws a line at the given height. Defaults heights are 5%,
Peak Highlight Do not highlight peaks The identified peak will not be shaded in any pane unless it
has the focus
Highlight identified peaks in all The identified peak will be shaded in all sub-panes
plots
5.4.13.12.6Peak Label

defined formula.
5.4.13.12.7Peak Windows
This section defines the caption that will be displayed in the MS Components plot peak window indicator. Caption can be
following sections:
• General (7.2)
• Sequence (7.3)
• Injection (0)

Component table windows Show component table windows Shows the component retention time window

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Other options Show all peak window drop lines Shows the peak window start and stop times as dashed lines
on the MS Component plot
Font Defines the font for component table window indicator
5.4.13.12.8Comparison
This section defines how MS Components plot overlays are displayed. The following options are available:

Arrangement Overlaid All overlaid MS Component plots are shown in one window.
Stacked All overlaid MS Component plots are shown in stacked
windows.
Overlay order Sorted by injection list order Not applicable for MS Component Plots
Current chromatogram always on Not applicable for MS Component Plots
top
selected.
selected.
right signal axis.
Mirror last overlaid chromatogram Plots the last confirmation peak mirrored against quantitation
and all other confirmation peak(s) (if applicable).
Internal Standard Show the XICs of the ISTD When checked, the quantitation and confirming ion plots for
associated with the component. the ISTD of a component are also plotted.
5.4.13.12.9Reference Injection
This section defines an optional reference injection which can be used for scaling and overlays.:

Specify dynamic or fixed injection Use injection in current sequence If selected, one can specify a series of rules to choose the
that matches this rule injection of interest. If multiple injections match the rule, then
one can further specify the first, most recent or last matching
injection be used.
Use fixed injection from arbitrary If selected, the browse button may be used to navigate to an
sequence injection in a sequence from elsewhere in a data vault.
Options Show as an overlay in every If selected, then the data from the specified reference injection
component tile is plotted as an overlay on each data tile.
Show as a separate component If selected, then the data from the specified reference injection
tile in the first position of the view is plotted in a separate tile in the upper left position of each
pane or plot group of tiles.
5.4.13.12.10 Events
MS Components plot. The following options are available:

Detection Parameters Show detection parameters Indicates the Detection Parameters.
5.4.13.12.11 Spectral Thumbnails

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This section defines how spectral thumbnails should be displayed. The following options are available:

Show Thumbnails Automatic Displays the thumbnails only when the UV-Vis Spectra Plot is
also displayed.
UV Always displays the thumbnails if UV spectral data are
available.
Fluorescence Always displays the thumbnails if fluorescence spectral data
are available.
Amperometry Displays the thumbnails of any existing I-t plots in all channels.
MS Always displays the thumbnails if mass spectrum data is
available.
None Don’t display any UV spectra thumbnails in the
chromatogram.
Thumbnails Size Width Defines the width of the thumbnail in mm.
Height Defines the height of the thumbnail in mm.
Range Bars Draw average range bars Marks and labels the ranges from which bunched spectra
were taken in the chromatogram. The number of spectra
averaged within a range is displayed in parenthesis.

This section allows a consistent color scheme for the objects in the MS Components plot to be defined. The following items
• Chromatograms 1-8 • Peak delimiter • Peak separation
• Peak tangents • Peak width • Baseline
• Rider baseline • Free baseline • Raw data points
• Detection parameters • Selected peak
• Background • Peak label • Detection parameter label
• Selected peak • Selected peak label
5.4.13.12.13 SmartLink
This section defines how the SmartLink functionality applies to the MS Components plot
5.4.13.12.13.1 Link to Chromatogram

MS component traces within the chromatogram plot time range.
When the plot is linked, the plot pane splits into several panes to
show plots from multiple peaks
Chromatogram Overlays When this option is selected, the MS Components plot will adapt to
show the component traces for injections that are overlaid in the
chromatogram plot.
Multiple Peak Selection When selected, the components that are selected in the
chromatogram plot or pinned in the Components section of the
navigation pane define which peaks are displayed in the MS
Components plot
5.4.13.12.13.2 Link to Injection


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Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
list.
5.4.13.12.13.3 Display By


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Maximum hit test distance Specifies the distance when the shape of the mouse pointer changes when tools
become available
The illustration shows the areas around the left and right peak delimiters of a peak
where the shape of the pointer changes to the shape of a tool. The smaller the hit
test distance a is, the smaller the area where the tool pointers appear.
Visualize selections Disables or enables visualization of selected objects (such as a selected peak),
(Not available for MS AutoFilters plots)
Highlight selected chromatogram Enables or disables the highlighting (bold) of the selected chromatogram.
5.4.14 Tentatively Identified Peaks Pane

Chromatograms of unknown injections in mass spectrometry (MS) data often contain peaks that are not identified by the
entries in the component table. Chromeleon can tentatively identify these peaks and estimate the amount value of each
peak using the nearest internal standard peak as a reference.
To tentatively identify the peaks, Chromeleon performs MS library screening on the apex spectrum of each unidentified peak
and determines the top twelve matches (hits) for each peak. The component name of the top match (hit #1) is assigned to
each peak.
The Tentatively Identified Peaks pane can be used to view or change the tentative identities. The columns in the pane
provide the following information for each tentatively identified peak: Retention Time, the name tentatively assigned to the
unidentified peak, the CAS number of the tentative component name, the estimated amount of the unidentified peak, Match
Factor (SI), Reverse Match Factor (RSI), Probability (%) (available for the Identity search type only), Library, and the internal
standard nearest to the unidentified peak.
You can change the tentative assignment of a peak by selecting another hit from the screening list, or by manually naming
the peak.
Right-clicking on a row will provide an option to move the peak and its component name from the Tentatively Identified
Peaks table to the processing method component table (thereby confirming the tentative assignment).
5.4.15 MS AutoFilters Pane

The MS AutoFilters pane allows a user to visualize all MS acquisition filters across single or multiple injections without
manually creating a channel from an XIC or an MS component in the component table. If a filter is of interest, a user is also
able to make a permanent channel from the filter.
5.4.15.1 Zooming and Navigating in the MS AutoFilters pane

The MS AutoFilters view allows zooming and navigating as required with the following options:

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available:
Autoscale Signal resizes the plot height to the data point with the highest intensity
currently visible
available:
Autoscale Time resizes the plot to the complete time range of the XIC as defined by
Double Click on the intensity axis Automatically resizes the plot height to the highest intensity data point currently
visible.
Double Click on the time axis Automatically resizes the plot width to the complete time range of the XIC as
defined by the processing method.
5.4.15.2 Copy
Copies a single selected MS acquisition filter chromatogram to the clipboard as an image This is also possible using the Ctrl
+ C hotkey.

Exports a single selected MS acquisition filter chromatogram to a text file. The following options are available:

Destination Clipboard Exports a textual description of the MS component trace into
the clipboard.
File Exports a textual description of the MS component trace into a
user defined text file.
Options Chromatogram data The exported MS component trace includes any corrections
such as a delay time or chromatogram subtraction.
Raw data The exported MS component trace is the raw data as
acquired without corrections
5.4.15.4 Create MS Channel

The function allows the user to create a permanent channel from the MS acquisition filter chromatogram. Selecting this
context menu item displays the following dialog with appropriate fields prefilled:

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Figure 48: Extract MS Channel
Trace Specify the chromatogram trace type to be extracted
TIC (Total Ion Current)—all ions matching the filter entered in the Filter list will be extracted from the
raw data.
Base Peak—base peak ions that match the filter entered in the Filter list will be extracted from the
raw data.
Mass Range—ions that match the filter entered in the Filter list and with a mass that matches the
mass or mass range entered in the Mass range(s) box will be extracted from the raw data.
Filter Specifies the acquisition filter from which the chromatogram will be extracted
Mass ranges Defines the mass, mass range, or a set of mass ranges to be extracted
Smoothing Specifies the type of smoothing to be performed on the chromatogram data when it is extracted.
Channel Name Defines the label that will be used to identify this extracted ion chromatogram in the channels list
Make channel permanent Creates a permanent channel when selected or if check box is clear a temporary channel is
created.
5.4.15.5 Properties
The following MS AutoFilters display options are available:


chromatogram plot.
5.4.15.5.2 Scale
This section defines the scaling behavior of the time axes for the MS AutoFilters plots.

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Time axis scale mode Full time range Displays the plot from t = 0min to the end of the acquisition
regardless of whether data was acquired during the entire
duration of the injection. Zooming functions are subsequently
synchronized between all plot time axes.
Extracted time range Displays the plot from the first point where data was acquired
to the last point where data was acquired. As MS filters are
often acquired during different retention time ranges,
subsequent zooming actions apply only to the selected plot.
5.4.15.5.3 Peak Characterization

This section defines how detailed peaks are characterized in the MS AutoFilters plots. Peak characterization is shown only if
a valid processing method is available. The following options are available:

main peak.
rider peak.
Draw peak width at Shows peak widths.
Peak widths
Draws a line at the given height. Defaults heights are 5%,
5.4.15.5.4 Peak Label


defined formula.

This section allows a color scheme for the objects in the MS AutoFilters plot to be defined. The following items can have
their line color defined:

• Baseline • Rider baseline • Free baseline
• Peak tangents • Peak width • Raw data points

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• Detection parameters • Raw data points • Selected Peaks

• Selected peak • Selected peak label

MS acquisition filters within the chromatogram plot time range.
Chromatogram Overlays When this option is selected, the MS AutoFilters plot will adapt to
show the MS acquisition filters for injections that are overlaid in the
chromatogram plot.
Multiple Peak Selection This option has no effect on the MS AutoFilters plot.
which filters are shown in the MS AutoFilters plot.

This section defines what optional zoom/unzoom tools are displayed on the MS AutoFilters plot
5.4.15.5.8 AutoFilter Filtering

This section defines the refined MS acquisition filter list to be displayed
Precursor Mass Defines the precursor mass of MS2 based acquisition filters to be displayed on the
MS AutoFilters plot
XIC Mass(es) or Range(s) Defines the product mass of MS2 or target mass of MS1 based acquisition filters to
be displayed on the MS AutoFilters plot.
Filters to be displayed (Read Only) Displays the refined or full list of filters that is currently being displayed
on the MS AutoFilters plot.
5.4.16 SmartLink
In the Data Processing Category, it is possible to link the following panes interactively to the chromatogram and/or the
injection list:
• Interactive Results (section 5.4.9)
• Interactive charts (section 5.4.4)
• MS components (section 5.4.13)
• Calibration plot (section 5.4.2)
• Spectral plots (UV-VIS (section 5.4.6), Fluorescence (section 5.4.7), I-t (section 5.4.8), MS (section 5.4.12)
The specific available options depend on the respective pane. Please refer to the corresponding section for details.
5.4.16.1 Chromatogram Linking

If the chromatogram plot is modified to show only certain peaks or injections, the linked panes will interactively adapt to
show only these peaks or injections. When the calibration plot, spectral plot, or I-t plot is linked, the plot pane splits into
several panes to show plots from multiple peaks.

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The following SmartLink options are available:
Link to Chromatogram Allows multiple peaks to be included in the array of SmartLink objects
Chromatogram Overlays Injections that are overlaid in the chromatogram plot for comparison define which injections are displayed in
the linked objects.
Multiple Peak Selection Peaks that are selected in the chromatogram plot or in the Components group on the Navigation Pane define
which peaks are displayed in the linked objects.
Zoom Area Zoom area of the chromatogram plot defines which peaks are shown in the linked objects.
5.4.16.2 Injection Linking

When injection-based linking is enabled, the linked panes will interactively adapt to show data from all of the injections
specified in the SmartLink settings (below)

Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]

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list.
5.4.16.3 Display By
5.4.17 On-Demand View Updating

In order to improve software responsiveness when working with large MS sequences containing many XICs, a new
sequence property (see 4.3.2) is now available to defer real-time updating of data and results in calculation intensive panes
of the Chromatography Studio. The option applies to both the Data Processing and Report Designer categories of the
Studio.
When the Sequence property “Update Views for MS Data” is set to “On-demand”, the following changes in Studio behavior
will occur:
5.4.17.1 Views
Calculation-intensive panes of the Studio will have a “View Out Of Date” watermark when the sequence is opened in the
Studio, as well as when changes have been made to the processing method or injection information. The panes will be
refreshed with current results when the user triggers an update (see next two sections)
5.4.17.2 Message Bar

When one or more visible panes has a “View Out Of Date” watermark, the Studio Message Bar will be displayed, notifying
the user of this situation. The Studio Message Bar will also include a hyperlink to initiate reprocessing of the data and
updating of the view panes.
5.4.17.3 Ribbon Bar

When one or more visible panes has a “View Out Of Date” watermark, the ‘Data Processing Home’ Ribbon of the Ribbon
Bar will include controls to initiate reprocessing of the data and updating of the view panes.
5.5 Non-Targeted MS Processing Category

5.5.1 Ribbon Bar
In the Non-Targeted MS Processing category, the buttons on the “Panes” section of the ribbon allow showing or hiding of
panes. The following panes are available:
• Processing (see section 5.5.2)

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• Frame Plot (see section 5.5.3)

• Frame Report (see section 5.5.4)
• Chromatogram Plot (see section 5.5.5)
• Mass Spectra (see section 5.5.6)
5.5.2 Processing Pane
Note: This pane is only available via the Non-Targeted MS Processing category (see section 5, 1.d.).
The Processing pane serves as the central point to control and monitor data processing of the Non-Targeted MS
Processing category. This is divided into 4 tabs: Setup, Preparation, Alignment, and Detection. The Non-Targeted MS
processing workflow is such that a user would typically setup processing parameters on the Setup tab, then either Start
processing the entire workflow or execute each of the steps (Preparation, Alignment, and Detection) manually. The tabs are
described below.
5.5.2.1 Setup
Setup is used to define processing parameters for Non-Targeted MS Processing. The parameters are stored as part of the
Chromeleon Processing Method.

Relative Integer Defines the injection number to use as a reference for Non-
Fixed Targeted MS Processing. Use of this option will allow the
processing method to be used with other sequences and maintain a
reference injection at the user defined position within the sequence.
Selection of this parameter and/or sub parameter will result in
generation of suggested default frame parameters.
Path Defines a static reference injection inside or outside of the sequence
to be used for Non-Targeted MS Processing. Use defines an
explicit injection that will always be referenced independent of the
sequence the processing method is associated with.
Selection of this parameter and/or sub parameter will result in
generation of suggested default frame parameters.
m/z Min Defines the start of the m/z range in which the algorithm is permitted
to create a frame.
m/z Max Defines the end of the m/z range in which the algorithm is permitted
to create a frame.
m/z Width [ppm] Defines the m/z width, in ppm, of a frame that is created to evaluate
whether signal meets or exceeds the peak intensity threshold.
This combined with Frame Time Width defines the rectangular size
of the frame.
Retention Time Start [min] Defines the start time of the range in which the algorithm is
permitted to create a frame.
Retention Time Stop [min] Defines the end time of the range in which the algorithm is permitted
to create a frame.
Frame Time Width [min] Defines the retention time width, in min, of a frame that is created to
evaluate whether signal meets or exceeds the peak intensity
threshold. This combined with m/z Width defines the rectangular
size of the frame.
Max. Number of Frames Defines the maximum number of frames the algorithm will detect
before stopping. The software maximum is 16000.
Peak Intensity Threshold Fixed Defines the minimum signal intensity in a frame in order to
designate a frame as valid.

Chromeleon 7

Auto-compute Calculates the minimum signal intensity in a frame in order to
designate a frame as valid based on a selected value
•TIC – percent of total ion intensities of the injection
•BPC – percent of the base peak of the injection
•Reference TIC – percent of total ion intensities of the
reference injection
•Reference BPC – percent of the base peak of the reference
injection
Scan Filter(s) List of Full Scan MS Filters Selection defines which MS filter TICs the algorithm is allowed to
evaluate and create frames for.
Advanced Opens advanced parameters for Non-Targeted MS Processing.
Reset Resets the frame parameters to suggested defaults.

Start Starts processing the injection workflow from Preparation through
Detection.
Options in the dialog displayed when the Advanced button is clicked are described below
Description User defined description of the experiment – meta data which has no effect on results.
Max Threads Maximum number of logical CPU cores the algorithm will use for computation.
Alignment Bypass Defines whether the alignment step of the Preparation, Alignment, and Detection workflow will be executed or
skipped.
Alignment Min Intensity Minimum intensity threshold for alignment.
CorrelationBinWidth Comparison width at the mass spectra level between reference and unknown injection used for data point
correlation for TIC alignment.
Max RT Shift Maximum allowable retention time shift of a datapoint when aligning an unknown against a reference TIC.
Tile Size The initial size of a correlation tile in number of scans for base peak alignment. Increased computing power
and memory are required for larger tile size values.
5.5.2.2 Preparation
Preparation is used to manually cache injections for Non-Targeted MS Processing and/or monitor the progress of caching.
This tab displays information only for the selected injection.
5.5.2.3 Alignment
Alignment is used to manually start alignment of an unknown TIC against a reference TIC as defined by the processing
method independent of the overall workflow and/or monitor the progress of alignment. This tab displays information only for
5.5.2.4 Detection
Detection is used to manually start valid frame detection in the unknown or reference TIC and/or monitor the progress of
detection. This tab displays information only for the selected injection.
5.5.3 Frame Plot Pane
The Frame Plot displays the reference, unknown aligned, and unknown unaligned XICs. At any given time, only 1 frame
can be displayed. This is defined by the frame selected in the navigation pane or in the Frame Report pane. The datapoints
are indicated with a small vertical dash. Left clicking on the plots will display the mass spectrum for the selected data point.
Ctrl + left clicking will display multiple mass spectra simultaneously. The plot controls for zooming and panning are identical
to the Chromatogram plot object.
The Frame Plot ribbon controls which are new are defined below. Please see section 5.4.1 for details on other controls.
Entries shared with the Frame Plot context menu are noted as such

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Data Reference Toggles display of reference XIC on the frame plot
Unaligned Toggles display of the unaligned unknown XIC on the frame plot
Remove Spectra Toggles display of the aligned unknown XIC on the frame plot
(available in Frame Plot pane context menu).
5.5.3.1 Scale
This section allows the user to define the scaling used for the time (X) and signal count (Y) axes of the frame plot. The

Time axis From Defines the start retention time of the frame plot X-axis
To Defines the end retention time of the frame plot X-axis
Autoscale Automatically defines the retention time range of the frame
plot X-axis
Intensity Axis From Defines the lowest signal count value of the frame plot Y-axis
To Defines the highest signal count value of the frame plot Y-axis
Autoscale Automatically defines the signal count range of the frame plot
Y-axis.

This section allows the user to define the displayed properties of the frame plot.

Axes Time axis Enables or disables the X-axis of the frame plot
Intensity axis Enables or disables the Y-axis of the frame plot
Font Defines font style, size and font emphasis of the axes
Axis to plot gap Defines distance between plot and axis
Frame Enables or disables a black border around the frame plot
Axis Titles Axis titles Enables or disables axis labeling
Units Enables or disables axis units labeling
Font Defines font style, size and font emphasis of the axis titles
Grid Horizontal grid lines Enables or disables horizontal grid lines in the frame plot
Vertical grid lines Enables or disables vertical grid lines in the frame plot
5.5.3.3 Title
This section allows the user to define the displayed titles of the frame plot.

Title Draw titles Enables or disables the titles displayed above the frame plot
Font Defines the font style, size, and emphasis of the titles
Legend Draw legend Enables or disables the frame plot legend
5.5.3.4 Data
This section allows the user to define the type of data displayed on the frame plot.

Reconstructed Ion Chromatogram Draw reference Enables or disables display of the reference injection XIC
Draw unaligned Enables or disables display of the unaligned unknown XIC

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Thumbnails Show spectral thumbnails Enables or disables thumbnails of mass spectra displayed on
Mass Spectra pane

This section allows the user to define which interactive controls on the plot are displayed on the frame plot.

Interactive Settings Show overview plot Enables or disables the miniature full frame plot view when
zoomed in on the main frame plot
Show popup controls Enables or disables the zoom and resize controls when
mousing over the lower left corner of the plot or in the center
of the frame axes
5.5.4 Frame Report Pane
The Frame Report pane consists of 2 sections – the Frame Table and the Frame Filter (see section 5.5.4.1). There is a
dedicated Interactive Results pane (see section 5.4.9) for Non-Targeted MS Processing. The report columns available for
display are listed in section 7.37. See section 5.4.9 for more information regarding the operation and functionality of
interactive results.
The Frame Table and Frame List in the Navigation Pane are updated dynamically based on the Frame Filter applied which
can be accessed and exposed from the bottom of the Frame Report Pane by clicking on the chevron or by editing the
Frame Table properties. The behavior is described in more detail in section 5.5.4.1.
5.5.4.1 Frame Filter

The Frame Filter and the Frame Filter table property in the Frame Report pane serve the same purpose.

Custom Conditions ALL Restrict the data shown based on comparing all rules with
user-defined numerical values and using the following logical
arguments:
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is between
Is not between
ANY [Any field from the sequence As for the previous parameter.
table – including user defined
columns]
and Forces matching based on every rule in the list. The or sub
parameter overrides the requirement to match every
comparison in the specific rule list.
5.5.5 Chromatogram Plot Pane
The Chromatogram Plot consists of a subset of functions from the Chromatogram pane used in the Data Processing
category of the studio. See section 5.4.1 for details.

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5.5.6 Mass Spectra Pane

Mass Spectra pane allows user to view the mass spectra for a selected Frame in the Frame Plot
5.5.7 Processing Parameters Pane
Note: This pane is only available via the Non-Targeted MS Processing category
The Processing Parameters pane shows the parameter values that were used to process each individual injection. This is a
read-only pane that shows the values for parameters that were defined in the processing method, but were subject to
change based on the actual data for that injection
Parameter Sub - Parameter Shown

Global Setting Description
Max Threads
Relative Reference Injection

Alignment Parameters Alignment Bypass
Alignment Min Intensity
Correlation Bin Width
Max RT Shift
RT Limits for Alignment
Tile Size
Frame Parameters Frame Time Width [min]
m/z Max
m/z Min
m/z Width [ppm]
Maximum Number of Frames
Peak Intensity Threshold
Retention Time Start [min]
Retention Time Stop [min]
Scan Filter(s)
Additional Parameters Injection
KM Clusters
PCA Process
5.6 Intact Protein Deconvolution Category

5.6.1 Ribbon Bar
The Ribbon bar provides access to various panes, method creation, and data processing.
In the Intact Protein Deconvolution category, the buttons on the “Panes” section of the ribbon allow showing or hiding of
panes. The following panes are available:
• Processing Method (see section 5.6.2)

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• Processing Parameters (see section 5.6.3)

• Component Results (see section 5.6.4)
• Chromatogram (see section )
• Deconvoluted Spectrum (see section 5.6.6)
• Source Spectrum (see section 5.6.7)
5.6.2 Processing Method Pane
Note: This pane is only available via the Intact Protein Deconvolution category
The parameters on this pane will be used to deconvolve the injection data. They are stored as part of the overall
Chromeleon processing method. It is divided into 4 tabs: Chromatogram Parameters, Source Spectra Parameters,
Algorithm Parameters and Multiconsensus. The IPD processing workflow is such that a user would typically setup the
processing method and then select Start or Start All on the ribbon. The tabs in this pane are described below.
5.6.2.1 Chromatogram Parameters

Use Restricted Time Checked Parameters defined under Range Display Type are
used for calculations
Unchecked Full time scale is used for calculations
Range Display Type Scan Range Uses the defined scan range for calculations
Time Limit Uses the time limit range for calculations
Chromatogram Settings m/z Range Mass range used in the calculation
Chromatogram Trace Type The type of Chromatogram used:
TIC Total ion intensity or
PBC Base Peak
Sensitivity Type of Sensitivity for the calculation

High or Low
Rel. Intensity Threshold (%) Intensity Threshold to be used in the calculation

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5.6.2.2 Source Spectrum Parameters

Source Spectra Parameters Sliding Windows Select this option to use the Sliding Windows deconvolution
algorithm to generate source spectra
Average over Selected Retention Time Select this option to use the Average over Selected Retention
Time deconvolution algorithm to generate source spectra
5.6.2.3 Algorithm Parameters

Deconvolution Algorithm ReSpect Isotopically Unresolved deconvolution algorithm
Xtract Isotopically Resolved deconvolution algorithm
Deconvolution Results Filter Output Mass Range Definable mass range for the output
Deconvoluted Spectra Display Mode Spectra will be displayable in either an Isotopic view or in
Mass Probability Distribution Profile
Charge State Distribution Model Mass Range Total Mass Range
Deconvolution Mass Tolerance Mass tolerance in either Da or PPM
Sensitivity Type of Sensitivity for the calculation
High or Low
Rel. Intensity Threshold (%) Intensity Threshold to be used in the calculation
Choice of Peak Model Intact Protein Appropriate peak model for the data. Peaks will be model
based on the intact protein model
Nucleotide Appropriate peak model for the data. Peaks will be model
based on the Nucleotide model
Resolution at 400 m/z Raw File Specific Resolution of the source spectrum at an m/z value of 400.
Method Specific
Generate XIC for each Checked XIC will be calculated for each component
Component
Calculate XIC
Unchecked XIC will not be calculated for each component
Advanced Settings Access to advanced parameters
5.6.2.4 Advanced Settings

Intact Protein Deconvolution Charge Carrier Number of adduct ions used during electrospray (ESI)
Parameters processing.
Charge High Maximum charge state to be deconvolved.
Charge Low Minimum charge state to be deconvolved.

End Time End time

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High Number of Adjacent Charges Maximum number of charge state peaks that must appear in
a row for components of the minimum output mass and
maximum output mass.
Intensity Threshold Scale Intensity threshold scale required to display peaks in a
chromatogram.
Low Number of Adjacent Charges Minimum number of charge state peaks that must appear in a
row for components of the minimum and maximum output
masses.
Min Peak Significance Numerical value (in standard deviations) that determines
whether a peak is considered legitimate and retained.
Negative Charge Whether the data was acquired in negative charge mode
during the electrospray (ESI) process.
Noise Compensation Whether the ReSpect algorithm improves signal detection
where the noise level varies across the data.
Noise Rejection Degree of confidence that a peak is plausible.
Number of Peak Models Number of peak models generated to determine the width that
a peak must have to be associated with a compound.
Peak Model Width Scale Number of regions used to determine the peak width required
for a peak to be associated with a compound.
Quality Score Threshold Minimum protein quality score required for a component to be
considered valid.
Relative Abundance Threshold Height of the smaller overlapping isotopic cluster used to
resolve overlapping isotopic clusters.
Start Time Start time
Target Peak Mass Expected target mass to use when calculating the peak
model.
Target Peak Shape Left Numerical value for the left side of the peak (determines the
peak sharpness required for a peak to be associated with a
compound).
Target Peak Shape Right Numerical value for the right side of the peak (determines the
peak sharpness required for a peak to be associated with a
compound).
5.6.2.5 Multiconsensus

Multiconsensus Injections Include Select the check box before an injection name to include the
injection in Multiconsensus deconvolution processing.
When the Multiconsensus result format is selected for

experiments with multiple loaded raw data files, Chromeleon
processes one experiment and then merges the
deconvolution results from all of the loaded raw data files
together.
Name The name of an injection in the current injection list of the
sequence.
Condition (Optional) Enter information about an injection. This
information is retained in list form. To assign an existing
condition to any other injection, click the down arrow for an
injection and select the preferred condition from the list.
Note: If you assign a condition to one injection, you must

assign a condition to all of the injections

Chromeleon 7

Multiconsensus Component Mass Tolerance Specifies the mass tolerance that components from individual
Merge files must satisfy to be merged into a Multiconsensus
component.
Click the down arrow to select the unit: ppm (parts per million)
or Da (Daltons).
RT Tolerance Specifies the maximum separation in retention time that
components from individual files must satisfy to be merged
into a Multiconsensus component.
Minimum Number of Required Specifies the minimum number of injections that must be
Occurrences included in a Multiconsensus component for it to be
considered valid.
5.6.3 Processing Parameters Pane
The Processing Parameters pane shows the parameter values that were used to process each individual injection. This is a
read-only pane that shows the values for parameters that were defined in Section 5.6.2, but were subject to change based
on the actual data for that injection

Chromatogram Parameters End Scan Number
End Time
Mass Range High

Mass Range Low
Start Scan Number
Start Time
ReSpect Parameters End Time
Start Time
Sliding Window Parameters Start Time
Stop Time
Xtract Parameters End Time
Start Time
5.6.4 Component Results Pane
The Component Results pane displays a nested table of the deconvolution results.
For non-Multiconsensus data, clicking the “+” icon next to a Result Component will expand the table to show a sub-table of
individual charge states and the associated results.
For Multiconsensus data, clicking the “+” icon next to a Result Component will expand the table to show a sub-table of the
results for the individual injections that were included in the multi-consensus experiment. Clicking the “+” icon next to an
injection will display a sub-table of the individual charge states and the associated results.
5.6.4.1 Table Columns

Chromeleon 7
Result Component Shows “Result Component 1” for the first component, “Result Component 2” for the second, and so on.
Monoisotopic Mass Displays a weighted average of the monoisotopic masses of each charge state
Sum Intensity Displays the sum of the intensities of the isotopic clusters in a charge state.
Relative Abundance Displays the relative abundance of the peaks in the sample that are above the threshold set by the Rel.
Abundance Threshold (%) (for Xtract) or Rel. Abundance Threshold (%) (for ReSpect) parameter.
Fractional Abundance Displays the fractional abundance of a component, which is the abundance for that peak relative to the
total abundance of all peaks in the spectrum, expressed as a percentage.
Score Displays the quality score of the deconvolved component.
Number of Charge States Displays the number of detected isotopic clusters for a given deconvolved mass.
This is the same number as the number of rows at the charge state level below the component level.
Charge State Distribution Displays the range of charge states detected for the component, from the lowest to the highest charge
state.
Mass Std. Dev. Displays the standard deviation, in Daltons, of the delta masses for all the charge states of a
component (for example, the standard deviation of Delta Mass (Da)).
Delta Mass Displays the difference between the mass of a specific component and the mass of the highest-
intensity component.
Start Time (min) Displays the start of the retention time range for of the Results Component in the selected injection
Stop Time (min) Displays the end of the retention time range for of the Results Component in the selected injection
RT Range Displays the range of the Results Component in the selected injection
Apex RT Displays the Apex RT of the Results Component in the selected injection
Number of Detected Intervals Displays the number of sliding windows within the specified tolerances where the application found the
component of interest
Scan Range (Visible only for sliding windows deconvolution experiments.) Displays the Start Time (min) for a
specific raw data file.
Protein Name The Protein Name variable returns the name of the target sequence that matches this component
within a given tolerance.
Modification Modification of the target sequence that best matches a specific component within a given tolerance.
Matched Mass Error (ppm) Error associated with the best target sequence that matches this component.
Theoretical Mass (Da) Theoretical mass of a component.
Drug Load Drug load of a component.
Average Charge The weighted average charge, based on abundance of each charge state
Monoisotopic Mass CV CV (coefficient of variation) of the monoisotopic masses for each charge state
Apex RT %CV CV (coefficient of variation) percentage of the apex retention time of a component.
Sum Intensity %CV CV (coefficient of variation) percentage of the apex intensities of a component.
Number of Files Observed Number of raw data files in which the component was detected.
Score %CV CV (coefficient of variation) percentage of the score of a component.
Condition Condition of a component.
5.6.4.2 Table Header Properties

Right-clicking on the table header provides access to a Properties dialog with the following tabs:
5.6.4.2.1 Table Columns…

Allows definition of which columns should be displayed and in which order. Note that this applies only to the main table, not
the injection or charge state sub-tables.
5.6.4.2.2 Remove Sort

Restores the sort order to the default order (by Results Component)
5.6.4.2.3 Filter Bar

Toggles display of an additional table row in the first position. To filter (limit) the display of the results rows to those meeting
specific criteria, type criteria in the cell

Chromeleon 7
5.6.4.2.4 Reset to Default Columns

Restores the table column configuration to the system default
5.6.4.3 Table Body Properties

Right-clicking on the table body provides access to a Properties dialog with the following tabs:
5.6.4.3.1 Copy
Copies the selected information to the clipboard
5.6.4.3.2 Add to Component Table

Adds a new entry to the MS Component Table of the Processing Method, based on the selected entry.
5.6.5 Chromatogram Pane
The Chromatogram pane displays the TIC or BPC Chromatogram and the Results XIC for a selected injection.
5.6.5.1 Zooming and Navigating

The chromatogram view allows zooming and navigating in the chromatogram as required with the following options:
Automatic Tool When active it is possible to zoom into the chromatogram by dragging an area. In
addition, other actions can be performed.
In addition the following zoom operations are available:

Double Click on the signal axis Automatically resizes the chromatogram height to the highest peak currently visible.
Double Click on the retention axis Automatically resizes the chromatogram width to the complete duration of the
chromatogram.
Signal axis zoom tools Shown when moving the cursor over the signal axis. The following functions are
available:
+ zooms into the chromatogram vertically
Autoscale Signal resizes the chromatogram height to the highest peak currently
visible
- zooms out of the chromatogram vertically
Retention time axis zoom tools Shown when moving the cursor over the retention time axis. The following functions
are available:
+ zooms into the chromatogram horizontally
Autoscale Time resizes the chromatogram to the complete duration of the
chromatogram.
- zooms out of the chromatogram horizontally
Full size button Shown when moving the cursor to the bottom left corner of the chromatogram plot.
Click the full size button to autoscale both axes simultaneously.

Right Click select Full Size Automatically resizes the chromatogram height to the full size.
Right Click select Autoscale Automatically resizes the chromatogram height to the highest peak currently visible.

Chromeleon 7
Right Click select Unzoom Reverts the recent zoom operation and returns to the previous view.
Holding down the right-hand mouse button and Zooms into the chromatogram area selected.
selecting an area of the chromatogram select Zoom
5.6.5.2 Properties
The following properties are available:

Axis to plot gap Defines the distance in mm between the axes and the
chromatogram plot.
Font Allows the font type and size of the axes titles to be defined.
Time axis grid lines Applies vertical grid lines to the chromatogram.
Orientation Horizontal Displays the chromatogram in the portrait orientation.
Vertical Displays the chromatogram in the landscape orientation.
5.6.5.2.2 Time Axis

This section allows the user to define the scaling used for the time axis. The following options are available:

Time Axis Share time axes If your chromatogram plot includes overlaid chromatograms
Fixed using Formula

Chromeleon 7

Tick mark intervals Fixed intervals of tick marks Defines whether tick marks should appear at selected intervals
5.6.5.2.3 Signal Axis

This section allows the user to define the scaling used for the signal axis. The following options are available.

Fixed using formula
Autoscale on peak
5.6.5.2.4 Title
following sections:
• Global Functions (see section 7.1)
• General (see section 7.2)
• Sequence (see section 7.3)
• Injection (see section 7.4)
• Chromatogram (see section 7.8)

Chromeleon 7
• Processing Method (see section 7.20)

• Custom Formulas (see section 5.7.27)

Title Draw Titles Displays chromatogram titles.
When checked the left part of the title can be defined
When checked the middle part of the title can be
defined based on formulas as described above.
When checked the right part of the title can be defined
Legend Draw legend Displays a legend for overlaid chromatograms.
When checked the format of the legend can be defined
based on formulae as described above.

• Chromatograms 1-8 • Peak width • Errors
• Free baseline • Triggers
• Peak tangents • Manual Commands

• Tube Label • Tubes • Fractions

This section defines the interactive settings in the chromatogram. The following options are available:
Maximum hit test distance Specify the distance when the shape of the mouse pointer changes when you
approach an object in the chromatogram plot.
Show overview plot When this check box is selected, the miniature overview of the chromatogram plot
Show popup controller When this check box is selected, the full size button, vertical and horizontal zoom

Chromeleon 7
Visualize selections When this check box is selected, visualization of selected objects, such as a
selected peak, is enabled.
Highlight selected chromatogram Enables or disables the highlighting of the selected chromatogram.
5.6.6 Deconvoluted Spectrum Pane
The Deconvoluted Spectrum pane displays the Deconvoluted mass spectrum for the selected injection.

available:
visible
available:
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click the full
visible.
5.6.6.2 Copy
Copies the mass spectrum plot to the clipboard as an image, This is also possible by using the Ctrl + C hotkey.


Chromeleon 7
the clipboard.
text file.
information
5.6.6.4 Full Size

Completely unzooms both the x-axis and y-axis
5.6.6.5 Autoscale Intensity

Completely unzooms the y-axis
5.6.6.6 Undo Zoom

Reverts the recent zoom operation and returns to the previous view.
5.6.6.7 Properties
5.6.6.7.1 Scale

range of the data



Chromeleon 7

Charge States Specifies if charge state lines should be superimposed on the
plot
5.6.6.7.3 Title

defined.
7.2.
Chromeleon 7.2.
7.2.

intensity axes

Chromeleon 7


defined:
• Grid lines • Axes • Spectrum 1-8

• Background

.
5.6.7 Source Spectrum Pane
The Source Spectrum pane shows the spectrum extracted from the source injection data. The charge states for the spectral
peaks are optionally overlaid on the plot.

available:
visible
available:
Full size button Shown when moving the cursor to the bottom left corner of the plot. Click the full

Chromeleon 7
visible.
5.6.7.2 Copy
Copies the mass spectrum plot to the clipboard as an image, This is also possible by using the Ctrl + C hotkey.


the clipboard.
text file.
information
5.6.7.4 Full Size

Completely unzooms both the x-axis and y-axis
5.6.7.5 Autoscale Intensity

Completely unzooms the y-axis
5.6.7.6 Undo Zoom

Reverts the recent zoom operation and returns to the previous view.
5.6.7.7 Properties
5.6.7.7.1 Scale

range of the data

Chromeleon 7



plot
5.6.7.7.3 Title

defined.
7.2.
Chromeleon 7.2.

Chromeleon 7

7.2.

intensity axes

defined:

• Background

5.7 Report Template

Report Template Files define how data will be printed. Figure 49 shows a typical report definition file.

Chromeleon 7
Figure 49: Report Template in the Chromatography Studio

All Chromeleon objects are highlighted using a red flag. Any cells containing user entered text or equations show no flags.
The following objects can be displayed in a report definition file:
5.7.1 Chromatogram Plot

The following display options are available for Chromatograms:
5.7.1.1 Plot Details

chromatogram plot.

Chromeleon 7
5.7.1.2 Time Axis


Fixed using Formula
5.7.1.3 Signal Axis


Fixed using formula
Autoscale on peak

Chromeleon 7

5.7.1.4 Title
following sections:
• Injection (see section 0)
Note: If a chromatogram is manually integrated the text “[manipulated]” is always shown in the left caption.

When checked the left part of the title can be defined based
When checked the format of the legend can be defined based
on formulae as described above.
5.7.1.5 Peak Characterization

This section defines how detailed peaks are characterized in the chromatogram plot. The following options are available:

Chromeleon 7

Peak delimiter N/A Shows the peak delimiters.
Separation Allows defining color and line style for the separation.
Baseline N/A Shows the baseline.
main peak.
rider peak.
Peak tangents N/A Shows the peak tangents.
N/A Allows defining color and line style for peak tangents.
Peak widths N/A Shows peak widths.
N/A Allows defining color and line style for peak widths.
10%, 50%.
Peak Highlight Do not highlight any peaks The identified peak will not be shaded unless it has the focus
Highlight all identified peaks All identified peaks will be shaded in all plots
Highlight all detected peaks All detected peaks will be shaded in all plots
5.7.1.6 Peak Label


defined formula.
5.7.1.7 Peak Purity

This section defines plot options for peak purity and peak match.

Peak Purity Index Overlay peak purity index Shows the peak purity index in the chromatogram plot.
Line Style Allows defining line color, width and style for the peak purity
index.
Peak Match Overlay peak match factor Shows the peak match factor in the chromatogram plot.
Line Style Allows defining line color, width and style for the peak match
factor.
5.7.1.8 Peak Windows

This section defines how peak windows are displayed.

Chromeleon 7

• Component (see section 7.28)

Component table windows Show component table windows Displays peak windows for components from the component
table (dotted lines indicating the width of the retention window
for the peak). Note: peak windows allow the retention time and
retention window of peaks to be adjusted graphically.
(Formula) Labels all peak calipers for identified peaks with details
Unidentified peak group windows Show unidentified peak group Displays peak windows for unidentified peak groups.
windows
(Formula) Labels all peak windows for unidentified peaks with details
Other Options Show all peak window drop lines Displays dotted lines for all peaks, not only the currently
selected peak.
Font Defines the font for peak windows.
5.7.1.9 Comparison
This section defines how chromatogram overlays are displayed. The following options are available:

Arrangement Overlaid All overlaid chromatograms are shown in one window.
Stacked All overlaid chromatograms are shown in stacked windows.
Grouped by detector All overlaid chromatograms from a given detector are shown in
one stripe.
Overlay order Sorted by injection list order Sorts the chromatograms in the order in which they occur in
the injection list
Current chromatogram always on Ensures that the current chromatogram is always at the front
top (overlaid) or the top (stacked).
selected.
selected.
right signal axis.
Mirror last overlaid chromatogram Mirrors the chromatogram that was added to the overlay last
on the time axis.
Peak Allows specification of the reference peak
Retention time Allows specification of the retention time to be used for
normalization

Chromeleon 7

Normalize time Allows to normalize the signal in x direction either by shifting or
stretching all chromatograms so that the retention time of the
selected component matches for each overlaid chromatogram.
First peak Allows specification of the start peak for normalization
Second peak Allows specification of the end peak for normalization
Normalize signal Off No signal normalization
Peak Normalizes overlaid signal to height of specified peak
Retention time Normalizes overlaid signal to height of a specific data point
Full range Normalizes overlaid signal to maximum peak height
Normalize time Off No normalization by time
Shift to peak Shifts the overlaid chromatogram to overlay a specific peak
Stretch between start and peak Stretches the overlaid chromatogram between the start and
specified peak
Stretch between two peaks Stretches the overlaid chromatogram between the two
selected peaks
Stretch between start and end Stretches the overlaid chromatogram between the start and
end, in order that the run times match
5.7.1.10 Events
chromatogram. The following options are available:

Detection Parameters N/A Indicates the Detection Parameters.
Gradients Dwell time Defines the dwell time. This will draw a gradient profile that is
in accordance with the retention time.
For this device only: Choose the device for which the gradients should be shown
for. By default, gradients are displayed for <All devices>.
Signal parameters N/A Displays signal parameters in the chromatogram.
Triggers N/A Hide or show triggers from the instrument method in the
chromatogram.
Manual commands N/A Displays manual commands in the chromatogram.
Errors N/A Displays errors in the chromatogram.
5.7.1.11 Fraction Tubes

This section defines how fraction tubes should be displayed. The following options are available:

Tubes Show tubes Displays the tubes collected
Label tubes Displays a label for the tube based on a formula using
Fractions Show fractions Displays the fractions collected
Hide tubes inside fractions Removes distinctions between tubes collected as part of the
same fraction
Label fractions Displays a label for the fraction based on a formula using
Label Style Font Allows the font type and size of the labels to be determined
Rotation Allows the orientation of the label to be determined
Alignment Allows the location of the label to be determined

Chromeleon 7
5.7.1.12 MS Quantitation Channel

This section defines special plot and display options to be applied when the MS Quantitation trace is displayed.

Trace visualization Trace offset If selected, each XIC is plot with a vertical offset compared to
the previous XIC; otherwise, all XICs are plotted on a common
using their true y-axis values
Show only display range of If selected, the XIC plot range is limited to the display range as
extracted ion trace defined in the component table of the processing method.
If not selected, the full-time range of the XIC is plotted.
Use alternating colors If selected, the XICs are drawn using a rotating color pallete
as defined in the Line and Fill Styles tab.
If not selected, the XICs are drawn using the primary plot
color, as defined in the Line and Fill Styles tab.
Show peak characterization If selected, the MS Quantitation plot is annotated with peak
characterizations (peak delimiters, peak tangents, baseline
and width.)
Label traces Label quantitation peaks Shows or hides the XIC peak labels
Label style Alignment Defines if the peak labels should be placed above the peak
apex or at the lower right of each peak trace.
Draw Frames If selected, a box is drawn around the peak labels
Font Defines the font for peak labels.
5.7.1.13 Channel
Allows selecting the channel for the chromatogram. The options are:
• Use channel selected at print time
• Fixed channel
5.7.1.14 Injection Overlay

Allows selection of an injection to be compared with the main chromatogram. The options are:

Dynamic overlays from current Add overlay rule Allows a rule for the overlay to be defined
sequence
Calibration standards Allows overlay of defined calibration standards. Options
available are: None, All, First, Recent and Last
Injection replicates Allows overlay of defined injection replicates. Options
available are: None, All, First, Recent and Last. The injection
can further be defined by a query (see section 4.4)
Empty injection query Allows overlay of an injection defined by a query. Options
available are: None, All, First, Recent and Last injection as
defined by a query. (see section 4.4)
Fixed injection and signal overlays N/A Allows selection of any injection and any channel from that
injection.
5.7.1.15 Channel Overlay

Defines which chromatograms will be overlaid
Specific channels and specific injections can be overlaid.


Chromeleon 7

5.7.1.17 SmartLink
Shows a list of all report objects that are linked with the chromatogram plot. An object can be unlinked by selecting the
object and clicking Unlink or pressing DELETE.
5.7.2 Calibration Plot

The following calibration plot display options are available:
5.7.2.1 Component

Component Use component selected at print Displays the calibration plot of the component selected at print
time time
Fixed component selected by Displays the calibration plot of the component with the selected
name name
Fixed component selected by Displays the calibration plot of the component with the selected
component table number component number.
Compatibility Option Use the first component in the Default option – If the “First Component Selected by Name”
component table if the specified option is enabled but if no associated component is found, the
component is not found. calibration curve is displayed for the first component in the list.
5.7.2.2 Channel
Allows selection of the channel for the calibration plot. The options are:
• Use channel selected at print time
• Fixed channel
5.7.2.3 Scale

Proportional N/A Allows the user to scale all plots proportionally to one another
when checked.
Amount Axis From Defines the start value of the amount axis.
To Defines the end value of the amount axis.
considered.
Logarithmic scale Applies the logarithmic scale to the amount axis.
Response Axis From Defines the start value of the response axis.
considered.

Chromeleon 7

Logarithmic scale Applies the logarithmic scale to the response axis.
Log-log linear transformation N/A Applies a log-log linear transformation to the current plot.

Axes Amount Axis Displays an amount axis on the calibration plot.
Response Axis Displays a response axis on the calibration plot.
Font Allows the font type and size of the axes to be defined
chromatogram plot.
Frame Allows the user to display the plot frame.
Axis Titles Axis Titles Applies titles to the calibration plot axes.
Units Displays units on the axes of the calibration plot.
5.7.2.5 Title
This section defines if and how titles should be displayed.

5.7.2.6 Options

Check Standard & Current Injection Draw check standard injection Draws points for check standard injection points on the
points calibration plot.
Draw level tolerance lines Displays concentration level tolerance lines on the calibration
plot when check standard/QC sample injection points are
displayed.
Draw response / amount Draws a horizontal line from the from the response axis
quantification lines of current (response value of the current injection). Where the line hits
injection the calibration curve, a vertical line is drawn to the amount
axis.
Confidence Interval Draw upper and lower confidence Draws the upper and lower confidence limits of the calibration
limits curve.

Chromeleon 7

Upper probability, Lower The confidence probability to be used when calculating the
probability confidence limits. The following values can be selected:
•95 %
•97.5 %
•99 %
•99.5 %
•99.9 %
•99.95 %
•99.995 %
Draw Hubaux-Vos detection limit Draws the Hubaux-Vos detection limits for the calibration
curve.

This section allows a consistent color scheme for the objects in the calibration plot to be defined. The following items can have their line color
defined:
• Grid • Markers • Original markers
• Axes • Selected marker • Hubaux-Vos lines
• Calibration curve • Disabled markers • Quantification lines
• Confidence interval curves • Check standard markers
• Prediction limit curve • Check standard outlier
markers
• Background
5.7.2.8 SmartLink

Select the chromatogram plot to link None No link is selected
with
Interactive Chromatogram Links with the interactive chromatogram in the data processing
category.
Chromatogram Plot (sheet name) Allows the user to link with a chromatogram plot on any other
sheet within the current report.
Multiple Peak Selection N/A Shows calibration plot for selected components
Zoom Area N/A Shows calibration plot for components whose peak apex is
within the zoom area.
5.7.3 UV-Vis Spectra Plot

The following peak spectra display options are available:
5.7.3.1 Spectra

Currently selected spectra N/A Peak and time spectra of current spectra plot.
(interactive mode only!)
Peak Spectra Name Displays the spectra plot for the peak of the selected name.
Greatest height Displays the spectra plot for the peak with the greatest height.
Greatest area Displays the spectra plot for the peak with the greatest area.
Number Displays the spectra plot for the peak with the selected
number in the chromatogram.
Component table number Displays the spectra plot for the peak with the selected
number in the component table.

Chromeleon 7

SLS hit number Displays the spectra plot for the peak with the selected SLS
hit number.
Time scans at fixed retention time N/A Displays the spectrum at a fixed retention time (or bunched
(or bunched over a range) over a time range).
5.7.3.2 Channel
This section defines which channel is shown. There are two options:
• Currently selected channel (interactive mode only!)
• Fixed Channel (Channel is specified by the user)
5.7.3.3 Scale

Absorbance From Defines the start value of the absorbance axis.


Absorbance axis Displays a response axis on the spectra plot.
Axis to Plot Gap Defines the distance in mm between the axes and the spectra
plot.
Frame Displays plot frame when selected
Orientation Horizontal Displays the chromatogram horizontally with respect to the
wavelength axis.
Vertical Displays the chromatogram vertically with respect to the
wavelength axis.
mAU.

Chromeleon 7

selected.
5.7.3.5 Title
This section allows controlling the titles for the spectral plot.

Title Draw Titles Displays UV-Vis spectral plot, mass spectral plot, or I-t plot
titles.
Center title Draw center title Displays the center part of the title.
When checked the center part of the title can be defined based

This section allows selecting which spectra should be shown.

Spectra Sampling Points Apex Spectrum Displays the spectrum at the peak apex.
ascending flank.
ascending flank.
tailing flank.
tailing flank.
Apex spectrum of recent The spectrum of the currently displayed peak is overlaid with
calibration standard the spectrum of the peak with the same name from the last
Apex spectrum of a fixed injection The spectrum of the currently displayed peak is overlaid with
selected injection.
Reference spectrum in The spectrum of the currently displayed peak is overlaid with
corresponding component table the reference spectrum from the component table of the
processing method.
Spectral library screening results The spectrum of the currently displayed peak is overlaid with
the spectra of the results of the spectral library screening (the
number of hits to be shown can be selected).
5.7.3.7 Label


Chromeleon 7

header.
5.7.3.8 Analysis

Difference Forms the difference between the main spectrum and the
remaining individual spectra of the pane. Depending on
representation of the difference spectra is in percent or in the
corresponding dimension; for example, mAU.
displayed.
spectrum displayed.
Overlay Overlay background spectra used Overlays the spectrum with the spectrum used for baseline
for baseline correction correction.
Overlay spectra without baseline Overlays each spectrum with the corresponding spectrum
correction without baseline correction.
5.7.3.9 Comparison
This section defines Arrangement, Offset, Overlay and Mirror settings.

Arrangement Stacked All overlaid spectra are shown in stacked plots
Overlaid All overlaid spectra are shown in one plot
Offset Scan offset Offsets the overlaid spectra by the scan value selected
Intensity offset Offsets the overlaid spectra by the intensity value selected
Overlay Overlay with right signal axis If selected the overlaid spectrum is measured against a right
signal axis.
Mirror Mirror signal If selected displays the overlaid spectrum as a mirror of
existing spectrum.

defined:
• Grid lines • Uncorrected spectrum • First front spectrum
• Axes • Spectrum 1-8 • Second front spectrum
• Reference Spectrum • Library Spectrum 1-7 • First tail spectrum
• Background spectrum • Apex Spectrum • Second tail spectrum
• Background

Chromeleon 7
5.7.3.11 SmartLink

with
category.
Multiple Peak Selection N/A Shows spectra for selected components
Zoom Area N/A Shows spectra for components whose peak apex is within the
zoom area.

Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]

Chromeleon 7

list.
5.7.4 Contour Plot

The following contour plot display options are available:
5.7.4.1 Scale

Time Axis From: Defines the start value of the time axis.
To: Defines the end value of the time axis.
scaled to show the whole chromatogram. This option is also
available in the layout ribbon.
Units Minutes [mins] or Seconds [s]
Scan Axis From: Defines the start value of the scan axis.
To: Defines the end value of the scan axis.
Autoscale When selected the contour plot and the spectra plot are scaled to
show the whole scan range. This option is also available in the
layout ribbon.
Signal Axis From: Defines the start value of the signal axis.
To: Defines the end value of the signal axis.
scaled to show the whole signal range.
Gradient Linear Scale Signal values are colored using a linear scale.
Logarithmic Scale Signal values are colored using a logarithmic scale. This option is
5.7.4.2 General

View 3D View Displays 3D contour view when selected
Data 3D data field If more than one type of 3D data field is available, the required field
can be selected from the list.
Axes Axis to plot gap Defines the distance in mm between the axes and the contour plot.
Font N/A Allows defining the font to be used for axes and labels in the Contour
Plot.

Chromeleon 7

Options Use black for zero Black represents a signal value of zero on the plot. This option
generates the fewest possible color repeats. A point’s color can
change when the scale changes.
Draw optimum integration path Draws the optimum integration path for the chromatogram (i.e. the
optimum wavelength profile). This option is also available in the
layout ribbon.
Spectra Retrieval Use raw spectra When selected raw spectra are shown and the UV settings from the
processing method are ignored. This option is also available in the
layout ribbon.
Apply baseline correction settings from When selected the settings selected on the UV Spectra tab page of
current processing method the processing method are applied to the raw data and include peak
spectrum bunching and baseline correction options. This option is
5.7.4.3 3D View Settings

Show Grid 3D View Shows a grid on the 3D plot.
Rotation X Type or select the angle of rotation around X axis of the 3D plot.
Y Type or select the angle of rotation around Y axis of the 3D plot.
Z Type or select the angle of rotation around Z axis of the 3D plot.
Reset Returns the axes to their default angles of rotation.
Performance N/A Best Quality using the same number of spectra used by the contour
plot. Best Performance using the fewest number of spectra.
5.7.4.4 Title

Draw titles Shows a title for the contour/3D plot.
Font Allows the font for the contour/3D plot title to be defined.
7.2.
Chromeleon 7.2.
7.2.
5.7.5 Mass Spectrum Plot

5.7.5.1 Spectra
This section defines which mass spectra are shown. There are three options:
• Currently selected mass spectrum (interactive mode only!)
• Peak spectrum (Peak is specified by the user)

Chromeleon 7
• Time Scan at a fixed retention time (as specified by the user)
5.7.5.2 Channel
5.7.5.3 Scale

Mass From Defines the start value of the wavelength axis.
Zero mass offset When selected a particular mass can be specified as the zero
mass which resets the masses of other ions relative to the
selected zero mass.
Intensity From Defines the start value of the absorbance axis.



Chromeleon 7

5.7.5.5 Title
This section allows controlling the titles for the mass spec plot.

defined.
7.2.
Chromeleon 7.2.
7.2.

This section allows selecting which auxiliary mass spectra should be shown.

Spectra Sampling Points Apex Spectrum Displays the mass spectrum at the peak apex as a thumbnail
Apex spectrum of recent The mass spectrum of the currently displayed peak is overlaid
calibration standard with the mass spectrum of the peak with the same name from
the last calibration standard injection of the sequence.
Apex spectrum of a fixed injection The mass spectrum of the currently displayed peak is overlaid
with the mass spectrum of the peak with the same name from
Spectral library screening results The mass spectrum of the currently displayed peak is overlaid
with the mass spectra of the results of the spectral library
screening (the number of hits to be shown can be selected).
5.7.5.7 Label
This section allows defining how labels are shown in the mass spectral plot.

Chromeleon 7
Peak Label Rotation Defines the angle the mass spectrum label is shown at.
Maximum threshold The threshold intensity (in %) at which mass peaks will be
labeled
Font Defines the font for the mass spectrum label.
Options Show baseline correction info Displays information about the baseline correction in the
header.
Show detected mass info for peak Checking this box will cause the detected mass for the peak
displayed.
Show detected mass info for time Checking this box will cause the detected mass for the time
displayed.
5.7.5.8 Analysis
This section controls how mass spectra analysis is performed.

Difference Forms the difference between the main mass spectrum and
the remaining individual mass spectra of the pane. Depending
on whether normalization is performed (see Frame & Axes),
representation of the difference mass spectra is in percent or
in the corresponding dimension;
Overlay Overlay background spectra used Overlays the mass spectrum with the mass spectrum used for
for baseline correction baseline correction.
Overlay spectra without baseline Overlays each mass spectrum with the corresponding mass
correction spectrum without baseline correction.
5.7.5.9 Comparison

intensity axes

defined:
• Axes • Spectrum 1-8 • First Tail spectrum

Chromeleon 7

• Background
5.7.5.11 MS Settings

TIC Spectrum Filter Filter This option works in combination with the Time Spectra Tool to
select a mass spectrum from a specific acquisition filter.
Select the acquisition filter in the Filter list (or type a filter definition),
and then use the Time Spectra Tool to select a retention time on the
chromatogram. The spectrum from the selected filter at the selected
retention time is shown on the plot.
If the selected filter was not in use at the selected retention time, the
spectrum at the retention time nearest to when the selected filter was
in effect is shown.
Noise Reduction Use setting of processing method Use the parameters from the MS Settings page of the processing
method.
Do not reduce Noise No noise reduction calculations will be performed
Relative Threshold Allows masses below a specified percentage of the base peak to be
ignored
5.7.5.12 Data Presentation

Plot Mode Automatic Select this option to display the mass spectral data in the format in
which it was acquired. For centroid format data, the plot displays a
discrete vertical line for each mass peak. For profile format data, the
plot is a continuous curve, with each mass peak consisting of
multiple data points.
Centroid Select this option to always display the data in centroid format, even
if profile data was acquired.
Mass precision N/A Select whether to use the mass precision defined on the MS
Settings tab page of the processing method, or to define a custom
number of significant figures to include in the mass peak labels on
the plot.
Mass tolerance N/A Select whether to use the default mass tolerance range defined on
the MS Settings page of the processing method, or to define a
custom range.
5.7.5.13 SmartLink
This section defines how the SmartLink functionality applies to the mass spec plot

spectra for peaks visible in the chromatogram plot. When the plot
is linked, the plot pane splits into several panes to show plots from
multiple peaks
plot define which peaks are displayed in the mass spec plot

Chromeleon 7
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Chromeleon 7
5.7.6 MS Components Plot

The following sections describe the tabs of the Properties dialogue accessed from the context menu.


chromatogram plot.
5.7.6.2 Time Axis

The time window for MS Component plots is defined in the component table of the processing method and cannot be
changed on this page. Separate time axes and tick mark intervals are not supported for MS Components. Please refer to
section 5.3.2.20 for more details.
5.7.6.3 Signal Axis


Range for component XICs Autoscale or Fixed Determines the method for selecting the range. Can be set to:
Autoscale or Fixed, Autoscale using reference injection or Fixed
Autoscale using reference using Formula.
injection
Fixed using formula
Fixed using Formula From Defines the start value of the signal axis using a report variable
formula
To Defines the end value of the signal axis using a report variable
formula
5.7.6.4 Title
This section defines the title that will be displayed in the chromatogram header. Left, middle and right titles can be selected
either based on simple text values or on user-defined formulas. The formula can be based on variables from the following
sections:
• General (7.2)
• Sequence (7.3)

Chromeleon 7
• Injection (0)

Legend Draw legend Displays the user-defined legend string in a legend box on the
MS Component plot.
5.7.6.5 Peak Characterization

This section defines how detailed peaks are characterized in the MS Components plot. The following options are available:

main peak.
rider peak.
Peak widths Shows peak widths.
Peak Highlight Do not highlight peaks The identified peak will not be shaded in any pane unless it
has the focus
Highlight identified peaks in all The identified peak will be shaded in all sub-panes
plots
5.7.6.6 Peak Label


Chromeleon 7

defined formula.
5.7.6.7 Peak Windows

This section defines the caption that will be displayed in the MS Components plot peak window indicator. Caption can be
following sections:
• General (7.2)
• Sequence (7.3)
• Injection (0)

Component table windows Show component table windows Shows the component retention time window
Other options Show all peak window drop lines Shows the peak window start and stop times as dashed lines
on the MS Component plot
Font Defines the font for component table window indicator
5.7.6.8 Comparison
This section defines how MS Components plot overlays are displayed. The following options are available:

Arrangement Overlaid All overlaid MS Component plots are shown in one window.
Stacked All overlaid MS Component plots are shown in stacked
windows.
Overlay order Sorted by injection list order Not applicable for MS Component Plots
Current chromatogram always on Not applicable for MS Component Plots
top
selected.
selected.

Chromeleon 7

right signal axis.
Mirror last overlaid chromatogram Plots the last confirmation peak mirrored against quantitation
and all other confirmation peak(s) (if applicable).
Internal Standard Show the XICs of the ISTD When checked, the quantitation and confirming ion plots for
associated with the component. the ISTD of a component are also plotted.
5.7.6.9 Reference Injection

This section defines an optional reference injection which can be used for scaling and overlays.:

Specify dynamic or fixed injection Use injection in current sequence If selected, one can specify a series of rules to choose the
that matches this rule injection of interest. If multiple injections match the rule, then
one can further specify the first, most recent or last matching
injection be used.
Use fixed injection from arbitrary If selected, the browse button may be used to navigate to an
sequence injection in a sequence from elsewhere in a data vault.
Options Show as an overlay in every If selected, then the data from the specified reference injection
component tile is plotted as an overlay on each data tile.
Show as a separate component If selected, then the data from the specified reference injection
tile in the first position of the view is plotted in a separate tile in the upper left position of each
pane or plot group of tiles.
5.7.6.10 Events
MS Components plot. The following options are available:

Detection Parameters Show detection parameters Indicates the Detection Parameters.
5.7.6.11 Component
This section allows defining of which component(s) should be displayed in the MS Components plot. The following options
are available:
Currently selected component(s) Displays the MS Components plot for the currently selected component in the navigation pane or
components dictated by SmartLink (if enabled).
Fixed component selected by name Displays the MS Components plot for the selected named component.
Fixed component selected by Displays the MS Components plot for the component matching the selected number in the
component table number component table.

This section allows a consistent color scheme for the objects in the MS Components plot to be defined. The following items
• Peak tangents • Peak width • Baseline
• Rider baseline • Free baseline • Raw data points
• Detection parameters

Chromeleon 7
5.7.6.13 SmartLink

Select the chromatogram N/A When a chromatogram in the dropdown is selected, the MS
plot to link with Components plot will adapt to show only the MS component traces
within the chromatogram plot time range. When the plot is linked,
the plot pane splits into several panes to show plots from multiple
peaks
Note: Interactive Chromatogram refers to the current

chromatogram of the Data Processing category.
Chromatogram Overlays When this option is selected, the MS Components plot will adapt to
show the component traces for injections that are overlaid in the
chromatogram plot.
Multiple Peak Selection When selected, the components that are selected in the
chromatogram plot or pinned in the Components section of the
navigation pane define which peaks are displayed in the MS
Components plot


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5.7.7 Injection Rack View

The following injection rack view plot options are available:
5.7.7.1 General
view.
zoom allows.)

Chromeleon 7
supported.
5.7.7.2 Title

5.7.8 Fraction Tray Plot

The fraction tray pane provides a graphical display of the fraction tube positions for the current sequence in the assigned
In the Fraction Tray plot properties dialog, there are several options:
5.7.8.1 General
view.
zoom allows.)
5.7.8.2 Title
5.7.8.3 Fill styles

In the fraction tray, the fill colors of various objects can be defined. The following options are available:
Tubes collected during sequence run N/A Defines the color for all tubes collected during the current sequence
Tubes collected from current injection N/A Defines the color for all tubes from the currently selected injection
Currently selected tube/fraction N/A Defines the color of the currently selected tube or fraction
5.7.8.4 Tooltip
Tooltip formula The content of the tooltip can be adapted depending on the context the Tray View

Chromeleon 7
5.7.9 Fluorescence Spectra Plot

The following fluorescence spectra display options are available:
5.7.9.1 Spectra

Currently selected spectra N/A Peak and time spectra of current spectral plot.
Peak Spectra Name Displays the spectra plot for the peak of the selected name.
Greatest height Displays the spectra plot for the peak with the greatest height.
Greatest area Displays the spectra plot for the peak with the greatest area.
Number Displays the spectra plot for the peak with the selected
number in the chromatogram.
Component table number Displays the spectra plot for the peak with the selected
number in the component table.
SLS hit number Displays the spectra plot for the peak with the selected SLS
hit number.
Time scans at fixed retention time N/A Displays the spectrum at a fixed retention time (or bunched
(or bunched over a range) over a time range).
5.7.9.2 Channel
5.7.9.3 Scale

Fixed intervals of tick marks Chromeleon automatically determines the interval of tick marks
(the small lines that mark values) on the time axis. To
intensity range of the spectrum.
Fixed intervals of tick marks Chromeleon automatically determines the interval of tick marks
(the small lines that mark values) on the time axis. To

Chromeleon 7


Intensity axis Displays an intensity axis on the spectra plot.
Axis to Plot Gap Defines the distance in mm between the axes and the spectra
plot.
wavelength axis.
wavelength axis.
mAU.
selected.
5.7.9.5 Title
This section allows controlling the caption for the spectral plot.

defined.
7.2.
Chromeleon 7.2.
7.2.
5.7.9.6 Spectra Filter

This section allows defining which fluorescence spectra are shown.

Chromeleon 7
Scan type Any Displays any spectrum found, regardless of the scan type.
Emission Displays emission scans only.
Excitation Displays excitation scans only.
Synchronous Displays synchronous scans only.
Photomultiplier Any Displays any spectrum found, regardless of which
photomultiplier tube (PMT) measured the spectrum.
Photomultiplier 1 Displays spectra measured by the primary PMT only.
Photomultiplier 2 Displays spectra measured by the secondary PMT only.
More Options N/A Adds additional filter criteria.
5.7.9.7 Overlay
This section allows selecting which spectra should be overlaid.

Reference Overlay None No reference overly is displayed.
Peak spectra of recent calibration The spectrum of the currently displayed peak is overlaid with
standard the spectrum of the peak with the same name from the last
Peak spectra of a fixed injection The spectrum of the currently displayed peak is overlaid with
selected injection.
5.7.9.8 Label

header.
5.7.9.9 Analysis

Difference Forms plots representing the difference between the main
spectrum and the remaining individual spectra of the pane.
Depending on whether normalization is performed (see Frame
& Axes), representation of the difference spectra is in percent
or in the corresponding dimension.
displayed.
spectrum displayed.
5.7.9.10 Comparison

Arrangement Stacked All overlaid spectra are shown in stacked plots

Chromeleon 7

Overlaid All overlaid spectra are shown in one plot
Offset Scan offset Offsets the overlaid spectra by the scan value selected
Intensity offset Offsets the overlaid spectra by the intensity value selected
Overlay Overlay with right signal axis If selected the overlaid spectrum is measured against a right
signal axis.
Mirror Mirror signal If selected displays the overlaid spectrum as a mirror of
existing spectrum.

defined:
• Axes • Spectrum 1-8 • First tail spectrum
• Background
5.7.9.12 SmartLink

with
category.
Multiple Peak Selection N/A Shows spectra for selected components
Zoom Area N/A Shows spectra for components whose peak apex is within the
zoom area.


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5.7.10 I-t Plot

The following I-t plot display options are available:
5.7.10.1 I-t Plots

Currently selected I-t plots N/A Peak and time scans of current I-t plot.
Peak I-t plots Name Displays the I-t plot for the peak of the selected name.
Greatest height Displays the I-t plot for the peak with the greatest height.
Greatest area Displays the I-t plot for the peak with the greatest area.

Chromeleon 7

Number Displays the I-t plot for the peak with the selected number in
the chromatogram.
Component table number Displays the I-t plot for the peak with the selected number in
the component table.
SLS hit number Displays the I-t plot for the peak with the selected SLS hit
number.
Time scans at fixed retention time N/A Displays the I-t plot at a fixed retention time (or bunched over
(or bunched over a range) a time range).
5.7.10.2 Channel
5.7.10.3 Scale

Apply scaling to all plots N/A Applies scaling to all I-t plots
Waveform Time From Defines the start value of the waveform axis.
To Defines the end value of the waveform axis.
waveform range of the I-t plot.
Current From Defines the start value of the response axis.
response range of the I-t plot.

This section defines settings for the axes, grid and normalization of the I-t plot.

Axes Waveform time axis Displays a waveform time axis on the I-t plot.
Current axis Displays a current axis on the I-t plot.
chromatogram plot.
Axis Titles Axis Titles Applies titles to the I-t plot axes.
Units Displays units on the axes of the I-t plot.
Grid Horizontal grid lines Applies horizontal grid lines to the I-t plot.
Vertical grid lines Applies vertical grid lines to the I-t plot.

Chromeleon 7

waveform time axis.
waveform time axis.
mAU.
Absolute Maximum Performs I-t plot normalization relative to the absolute
Relative Maximum Performs I-t plot normalization relative to the relative
Fixed Waveform Time at Performs I-t plot normalization relative to the fixed waveform
time point selected.
5.7.10.5 Title
This section defines the caption for the I-t plot.

Draw titles Shows a title for the I-t plot.
Font Allows the font for the I-t plot title to be defined.
7.2.
Chromeleon 7.2.
7.2.
5.7.10.6 Peak I-t Plots

This section defines which I-t plots are shown.

I-t plot Sampling Points Apex I-t plot Displays the I-t plot at the peak apex.
ascending flank.
ascending flank.
flank.
flank.
Reference Overlay None No reference overlay is displayed.
Apex I-t plot of recent calibration The I-t plot of the currently displayed peak is overlaid with the I-
standard t plot of the peak with the same name from the last calibration
standard injection of the sequence.
Apex I-t plot of a fixed injection The I-t plot of the currently displayed peak is overlaid with the I-
t plot of the peak with the same name from the selected
injection.

Chromeleon 7
5.7.10.7 Label
This section defines how labels are shown in the I-t plot.

Label Maxima Rotation Defines the angle at which the I-t plot label is shown.
Font Defines the font for the I-t plot label.
Options Show match factor Displays, in the caption for each I-t plot, the match factor for
that I-t plot relative to the corresponding main I-t plot. The main
I-t plot is either the peak I-t plot, or a reference I-t plot (I-t plot
comparison).
Show baseline correction info Displays information about baseline correction in the caption of
each I-t plot.
5.7.10.8 Analysis
This section controls how I-t plot analysis is performed.

I-t plot Analysis None No analysis is performed.
Difference Forms the difference between the main I-t plot and the
remaining individual I-t plots of the pane. Depending on
representation of the difference I-t plots is in percent or in the
corresponding dimension (nA).
First derivative Calculates and displays the first derivative of each I-t plot
displayed.
Second derivative Calculates and displays the second derivative of each I-t plot
displayed.
5.7.10.9 Comparison

Arrangement Stacked All overlaid I-t plots are shown in stacked plots
Overlaid All overlaid I-t plots are shown in one plot
Offset Scan offset Offsets the overlaid I-t plot by the scan value selected
Intensity offset Offsets the overlaid I-t plot by the intensity value selected
Overlay Overlay with right signal axis If selected the overlaid I-t plot is measured against a right
signal axis.
Mirror Mirror signal If selected displays the overlaid I-t plot as a mirror of existing
spectrum.

This section defines the color of each item in the peak I-t plot. The following items can have their color defined:
• Grid Lines • Uncorrected I-t plot • Second Front I-t plot
• Axes • I-t plot 1-8 • First Tail I-t plot
• Reference I-t plot • Apex I-t plot • Second Tail I-t plot
• Background I-t plot • First Front I-t plot
• Background
5.7.10.11 SmartLink

Chromeleon 7
5.7.10.11.1Link To Chromatogram

with
category.
Multiple Peak Selection N/A Shows I-t plot for selected components
Zoom Area N/A Shows I-t plot for components whose peak apex is within the
zoom area.
5.7.10.11.2Link to Injection

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Chromeleon 7

list.
5.7.10.11.3Display By
5.7.11 NTMS Frame Plot

The following sections describe the tabs of the Properties dialogue accessed from the context menu
5.7.11.1 Frame Filter

This section defines which frames are displayed in the plot:

Custom Conditions ALL Restrict the data shown based on comparing all rules with
user-defined numerical values and using the following logical
arguments:
Is equal to (=)
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Is not between
columns]
Or Allows for matching based on only one comparison in the rule
And Forces matching based on every rule in the list. The or sub
5.7.11.2 Scale
This section allows the user to define the scaling used for the time (X) and signal count (Y) axes of the frame plot. The

Time axis From Defines the start retention time of the frame plot X-axis
To Defines the end retention time of the frame plot X-axis
Autoscale Automatically defines the retention time range of the frame
plot X-axis
Intensity Axis From Defines the lowest signal count value of the frame plot Y-axis
To Defines the highest signal count value of the frame plot Y-axis

Chromeleon 7
Autoscale Automatically defines the signal count range of the frame plot
Y-axis.

This section allows the user to define the displayed properties of the frame plot.

Axes Time axis Enables or disables the X-axis of the frame plot
Intensity axis Enables or disables the Y-axis of the frame plot
Font Defines font style, size and font emphasis of the axes
Axis to plot gap Defines distance between plot and axis
Frame Enables or disables a black border around the frame plot
Axis Titles Axis titles Enables or disables axis labeling
Units Enables or disables axis units labeling
Font Defines font style, size and font emphasis of the axis titles
Grid Horizontal grid lines Enables or disables horizontal grid lines in the frame plot
Vertical grid lines Enables or disables vertical grid lines in the frame plot
5.7.11.4 Title
This section allows the user to define the displayed titles of the frame plot.

Title Draw titles Enables or disables the titles displayed above the frame plot
Font Defines the font style, size, and emphasis of the titles
Legend Draw legend Enables or disables the frame plot legend
5.7.11.5 Data
This section allows the user to define the type of data displayed on the frame plot.

Reconstructed Ion Chromatogram Draw reference Enables or disables display of the reference injection XIC
Draw unaligned Enables or disables display of the unaligned unknown XIC
Thumbnails Show spectral thumbnails Enables or disables thumbnails of mass spectra displayed on
Mass Spectra pane
5.7.12 NTMS Processing Parameters Table

The Processing Parameters pane shows the parameter values that were used to process the selected injection. These are
the values for parameters that were defined in the processing method, but were subject to change based on the actual data
for that injection

Global Setting Description
Max Threads
Relative Reference Injection

Alignment Parameters Alignment Bypass
Alignment Min Intensity
Correlation Bin Width
Max RT Shift
RT Limits for Alignment

Chromeleon 7

Tile Size
Frame Parameters Frame Time Width [min]
m/z Max
m/z Min
m/z Width [ppm]
Maximum Number of Frames
Peak Intensity Threshold
Retention Time Start [min]
Retention Time Stop [min]
Scan Filter(s)
Additional Parameters Injection
KM Clusters
PCA Process
5.7.13 IPD Chromatogram Plot

The following display options are available for IPD Chromatograms:
5.7.13.1 Select Component

Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
Variable Selects an IPD Results variable from the list.
= (is equal to)
< (is less than)
> (is greater than)
is between
is not between
is during previous
contains
does not contain
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ends with
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Chromeleon 7
Injection Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
= (is equal to)
< (is less than)
> (is greater than)
is between
is not between
is during previous
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does not contain
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ends with
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Total Number of Plots Specifies how many component XIC plots will be displayed
Show Chromatogram Trace Shows the TIC/BPC plot stacked above the component XIC
plot.

chromatogram plot.

Chromeleon 7
5.7.13.3 Time Axis


Fixed using Formula
5.7.13.4 Signal Axis


Fixed using formula
Autoscale on peak

Chromeleon 7

5.7.13.5 Title
following sections:

When checked the left part of the title can be defined based


Chromeleon 7

5.7.14 IPD Mass Deconvoluted Spectra Plot

This object shows the spectrum extracted from the source injection data. The charge states for the spectral peaks are
optionally overlaid on the plot.
5.7.14.1 Select Deconvoluted Component

Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
= (is equal to)
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> (is greater than)
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Chromeleon 7
Injection Components Match XXX of the following rules ALL is equivalent to the AND logical operator. Finds injections
= (is equal to)
< (is less than)
> (is greater than)
is between
is not between
is during previous
contains
does not contain
starts with
does not start with
ends with
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is not empty
Total Number of Plots Specifies how many component XIC plots will be displayed
Show Chromatogram Trace Shows the TIC/BPC plot stacked above the component XIC
plot.
5.7.14.2 Scale

range of the data

Chromeleon 7



5.7.14.4 Title

defined.
7.2.
Chromeleon 7.2.
7.2.
5.7.14.5 Comparison

Chromeleon 7

intensity axes

defined:

• Background
5.7.15 IPD Mass Source Spectra Plot

This object shows the spectrum extracted from the source injection data. The charge states for the spectral peaks are
optionally overlaid on the plot.
5.7.15.1 Scale

range of the data


Chromeleon 7

plot
5.7.15.3 Title

defined.
7.2.
Chromeleon 7.2.
7.2.
5.7.15.4 Comparison

intensity axes

Chromeleon 7


defined:

• Background
5.7.16 IPD Processing Parameters Table

The Processing Parameters pane shows the parameter values that were used to process the selected injection. These are
the values for parameters that were defined in the processing method, but were subject to change based on the actual data
for that injection.

Chromatogram Parameters End Scan Number
End Time
Mass Range High

Mass Range Low
Start Scan Number
Start Time
ReSpect Parameters End Time
Start Time
Sliding Window Parameters Start Time
Stop Time
Xtract Parameters End Time
Start Time
5.7.17 Result/Scatter Charts

The following display options are available for result charts:
5.7.17.1 Data Settings

Horizontal Axis Variable n.a. Displays horizontal axis variable that can be user defined
section 7.
Note: This option is only available for scatter charts.
Variables Chart Type Defines chart type. All chart types from section 5.7.17.2 are
available.
Chart Variable Defines chart variable that can be based on all report formulas
from all the areas detailed in section 7.
Style Defines color, line style and symbol type for the chart.

Chromeleon 7
Notes:
For the bubble chart type an additional Circle Diameter parameter is displayed, to define the bubble diameter.
For the High Low chart type, two additional lines are displayed, to define formulas used for start and end values.
For each selected Control Chart option (5.7.17.2) a line is displayed to define the formula.
5.7.17.2 Chart Type

The following chart types are available:
5.7.17.2.1 Scatter
• Scatter with lines • Scatter with splines
5.7.17.2.2 Line
• Line • Line with points • Spline with points
• Spline
5.7.17.2.3 Column
• Column • Stacked column (100%) • Stacked column 3D
• Stacked column • Column 3D • Stacked column (100%) 3D
5.7.17.2.4 Area
• Area • Stacked area (100%) • Stacked area 3D
• Stacked area • Area 3D • Stacked area (100%) 3D
5.7.17.2.5 Pie & Doughnut

• Pie • Pie 3D • Doughnut 3D
• Doughnut
5.7.17.2.6 Miscellaneous
• Bubble • Range Area • Column range 3D
• High Low • High Low 3D • Range area (100%) 3D
• Column Range
5.7.17.3 Filter Options – Injection Charts

Custom Conditions Only include injections that match Displays only injections that fulfill certain conditions, based on
the following conditions report variables.

Chromeleon 7

ALL (Any field from the injection Restrict the data points shown based on comparing the selected
list – including user defined variable with a user-defined value and using the following logical
columns) arguments:
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
5.7.17.4 Filter Options –Peak Charts

Identified Peaks Include Unidentified Peaks Shows all peaks that have not been identified.
Unidentified Peaks Include not identified peaks of the Shows all components of the component table that have not
component table been detected in the current injection.
Undetected components Reject peaks with a smaller Shows all components of the component table that have not
relative area than n % been detected in the chromatogram.
Custom Conditions Only include peaks that match the Displays only peaks that fulfill certain conditions, based on
following conditions report variables.

Chromeleon 7

ALL (Any field from the injection Restrict the data points shown based on comparing the
list – including user defined selected variable with a user-defined value and using the
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
5.7.17.5 Grouping Options – Injection Charts

Sort the injections according to injection Number Sorts the injections according to injection number.
evaluation of this formula Injections are grouped by the user-defined formula based on
5.7.17.6 Grouping Options – Peak Charts

Sort the peaks according to Peak Number Sorts the peaks according to peak number.
5.7.17.7 Title

Draw titles Displays results chart titles.

Chromeleon 7

Font Allows the font type and size of the titles to be defined.
section 7.
section 7.
section 7.

Axes Horizontal Axis Displays a horizontal axis on the results chart.
Vertical Axis Displays a vertical axis on the results chart.
Axes Description Draw Axes Title Applies titles to the results chart axes.
Units Displays units on the axes of the results chart.
Group labels Displays the group labels.
Horizontal Axis Label Formula Labels horizontal axis with details generated by the user-
defined formula based on all report formulas from all the areas
Grid Horizontal grid lines Applies horizontal grid lines to the results chart.
Vertical grid lines Applies vertical grid lines to the results chart.
5.7.17.9 Horizontal Axis

Range From Defines the start value of the horizontal axis. Either Auto or a
To Defines the end value of the horizontal axis. Either Auto or a
5.7.17.10 Vertical Axis

Settings for axis Determines the vertical axis for which to define the settings. To be
able to select between different vertical axes, you have to have at
least two chart variables.
Range From Defines the start value of the vertical axis. Either Auto or a specific
To Defines the end value of the vertical axis. Either Auto or a specific
5.7.17.11 Data Labels


Data Point Labels Draw Data Point Labels Labels all data points with details generated by the user-
defined formula.
Font Defines the font for data point labels.

Chromeleon 7

Chart variable name Displays the (short) name of chart variable in the label.
X value Displays x value of the data point (for scatter charts only).
Y value Displays y value of the data point.
Report Formula The formula can be based on variables from all the areas
Legend Show Legend Displays legend in the upper right corner of the chart. Options:
• Inside plot area
• Outside plot area
5.7.17.12 Statistics
Mean Displays a horizontal line at the average value of the data set.
Linear trend line Displays a linear trend line of the data set.
Show trend line formula includes the linear formula for the trend line in its data label
Font Defines the font for the labels.
5.7.17.13 Control Chart
Upper Limit Displays the line of the defined upper limit value or report formula.
Target Displays the line of the defined target value or report formula.
Lower Limit Displays the line of the defined lower limit value or report formula.
Font Defines the font for control chart labels.
Note: The Upper Limit, Target, and Lower Limit values or report formulas have to be defined on the Data Setting
properties page (4.7.4.1).
5.7.17.14 Appearance
This section allows a consistent color scheme for the objects in the results chart to be defined. The following items can have
their line color defined:
• Mean • 3s • Gridlines
• Linear Trend • Upper Limit • Minor Gridlines
• 1s • Target
• 2s • Lower Limit
• Back Interior • Chart Interior

Border Style n.a. Defines the border style for the results chart:
• None
• Emboss
Arrangement Overlaid All charts are shown overlaid.
Stacked All charts are shown stacked (above each other).
3D Mode n.a. Shows chart as 3-dimensional chart.

Chromeleon 7
5.7.17.15 SmartLink

with
category.
Chromatogram Plot (sheet name) Links with a chromatogram plot on any other sheet within the
current report.
Multiple Peak Selection N/A Shows I-t plot for selected components
Zoom Area N/A Shows I-t plot for components whose peak apex is within the
zoom area.
5.7.18 General Charts

It is possible to insert user-defined charts that display the data selected by the user. The following chart types are supported:
5.7.18.1 Scatter
• Scatter with lines • Scatter with splines
5.7.18.2 Line
• Line • Line with points
• Spline • Spline with points
5.7.18.3 Column
• Column • Stacked Column (100%) • Stacked Column 3D
• Stacked Column • Column 3D • Stacked Column (100%) 3D
5.7.18.4 Area
• Area • Stacked Area (100%) • Stacked Area 3D
• Stacked Area • Area 3D • Stacked Area (100%) 3D
5.7.18.5 Pie & Doughnut

• Pie • Pie 3D
• Doughnut • Doughnut 3D
5.7.18.6 Miscellaneous
• Bubble • Range Area • Range Area 3D
• High Low • High Low 3D
• Column range • Column Range 3D
5.7.19 Illustrations
It is possible to insert pictures from a file into a worksheet, or shapes can be used. The following illustration types are
supported:
5.7.19.1 Picture
Inserts a picture from a file.

Chromeleon 7
5.7.19.2 Shapes
• Line • Rectangle • Oval
5.7.20 Chromeleon Report Tables

Chromeleon report tables are designed to show groups of Chromeleon variables (see section 7) e.g. integration tables and
summary tables. The following tables are available.
5.7.20.1 Grouping Columns

For those tables that support grouping, the following group columns are available:
• Group Sum • Group Standard Deviation • Group Relative Range
• Group Count • Group Relative Standard Deviation • Group Minimum
• Group Average • Group Range • Group Maximum
When rows of the tables are grouped, the group columns display the calculated values for each row group. There are two
options when creating a group column:
1. Group the values in Column number x, where x is the number of a column in the table.
2. Group the values calculated by a user-defined formula.
5.7.20.2 Results – Integration Table

This table is designed to show results based on the chromatogram e.g. retention time, peak area, etc. An unlimited number
of columns can be created, and each column can show any variable shown in section 7. The details in this table change,
depending on which injection is being viewed.
The following properties can be defined for the report:
5.7.20.2.1 Table Channels
Single channel Lists peaks of a single (currently active or specific) channel
Multiple channels Lists peaks of one or more specific channels
Channels of detector Lists peaks of al channels of selected detectors
5.7.20.2.2 Filter Peaks

Undetected Components Includes rows for components of the Component Table that
have not been detected in the current injection.

Chromeleon 7

ALL (Any field from the sequence Restrict the data points shown based on comparing the
table – including user defined selected variable with a user-defined value and using the
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
5.7.20.2.3 Grouping Options

Sort the report table according to Retention time of peak Sorts the table according to peak retention time.
evaluation of this formula Peaks are grouped by the user-defined formula.
Report only the last row for each Reports only the last row of each group.
group
Ignore case when comparing text Ignore case when comparing text results.
results
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6
Evaluate for channel Channel used for sorting.
Group columns for fixed channels Channel Groups report columns by channel.
by
Report Variable Groups report columns by report variable.
5.7.20.2.4 Report Column

Column Management N/A Manages report columns.
Inserts new report column before selected.
Appends new report column at the end of the table.
Removes selected report column.
Selects previous report column.
Selects next report column.

Chromeleon 7

Column Properties Formula Defines content of report column by selecting a report variable
formula. This formula can be based on report variables from
all categories detailed in section 7.
Header Defines the report column header.
Unit Defines the unit.
Format Defines the number or date format for displaying results.
Channel Defines whether report columns display peak results from
multiple channels. This depends on the corresponding
settings on the Table Channels tab (section 5.7.20.2.1).
Selected Channel: Displays values of currently selected
channel.
All Channels: Displays values of all table channels in one
column per channel.
Highest Response: Displays values of the detection channel
where a peak shows the highest response.
Highest Response per Detector: Displays values of the
detection channel where a peak shows the highest response
for each detector in one column per detector.
Quantitation Channel: Displays values of the channel selected
for quantitation of the component, defined in the processing
method.
Fixed Channel: Displays values of the detection channel as
defined here.
Advanced Column Properties N/A Defines content for additional header rows as selected on the
Header Rows tab (section 5.7.20.2.5).
Channel Row Defines content of Channel header row.
5.7.20.2.5 Header Rows
Channel Displays an additional channel header row.

Select the chromatogram plot to link N/A Links integration table to a selected chromatogram plot.
with
Multiple Peak Selection Selected peaks define which peaks are displayed in the table.
Zoom Area Chromatogram zoom area defines which peaks are displayed
in the table.
5.7.20.2.7 Multiple Component Assignments

If a peak is assigned to multiple components the result row of this peak is repeated for every assigned component. The
basis peak results as peak area, height, etc… will be identical in every row but the component based results as amount or
calibration related results will depend on the corresponding component.
5.7.20.3 Results – Peak Summary Table

This table is designed to show a summary of the results from all the chromatograms in the sequence e.g. retention time,
amount, etc. An unlimited number of columns can be created, and each column can show any variable from those sections
detailed in section 7. The details in this table do not change if different chromatograms are selected.
5.7.20.3.1 Filter Injections


Chromeleon 7

Custom Conditions ALL (Any field from the sequence Restrict the data points shown based on comparing the
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
columns]

Sort the report table according to default order for injections Sorts the table according to injection number
evaluation of this formula Peaks are grouped by the user-defined formula
group
Ignore case when comparing text Ignore case when comparing text results
results
Use Chromeleon 6 Sort Order Uses the sort order used in Chromeleon 6


Chromeleon 7

Channel Defines from which channel the report column displays peak
results.
channel.
defined here.
Component Defines from which component the report column displays
peak results.
Selected Component: Displays values of currently selected
component.
Fixed Component: Displays values of the component as
defined here.
Component Row Defines content of Component header row.
Component Displays an additional component header row.

Select the chromatogram plot to link N/A Links peak summary table to a selected chromatogram plot.
with
Chromatogram Overlays Chromatogram overlays define which injections are displayed
in the table.
5.7.20.4 Results – Consolidated Table

This table is designed to show results based on the peaks in the chromatograms in rows and the results from injections in
the sequence in columns, e.g. retention time, peak area, etc. An unlimited number of columns can be created, and each
column can show any variable shown in section 7.
5.7.20.4.1 Filter Injections


Chromeleon 7

Custom Conditions Only include injections that match Displays injections that fulfill a certain condition.
the following conditions
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]
5.7.20.4.2 Table Channels
Single channel Lists peaks of a single (currently active or specific) channel
Multiple channels Lists peaks of one or more specific channels
Channels of detector Lists peaks of all channels of selected detectors
5.7.20.4.3 Filter Peaks

Undetected Components Includes rows for components of the Component Table that
have not been detected in the current injection.

Chromeleon 7

Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
columns]

Sort the report table according to Retention time of peak Sorts the table according to peak retention time.
evaluation of this formula Peaks are grouped by the user-defined formula.
group
results
Evaluate for channel Channel used for sorting.
Group columns for fixed channels Injection Groups report columns by injection.
by
Report Variable Groups report columns by report variable.


Chromeleon 7

Injection Defines whether report columns display peak results from
multiple injections. This depends on corresponding settings on
the Filter injection tab (section 5.7.20.4.1).
First Injection: Displays values of first injection a result is found
for the respective peak.
All Injections: Displays values of all table injections in one
column per injection.
Channel Defines whether report columns display peak results from
multiple channels. This depends on the corresponding
settings on the Table Channels tab (section 5.7.20.4.2).
channel.
All Channels: Displays values of all table channels in one
column per channel.
Highest Response: Displays values of the detection channel
where a peak shows the highest response.
Highest Response per Detector: Displays values of the
detection channel where a peak shows the highest response
for each detector in one column per detector.
Quantitation Channel: Displays values of the channel selected
for quantitation of the component, defined in the processing
method.
defined here.
Injection Row Defines content of Injection header row.
Injection Displays and additional injection header row.

Select the chromatogram plot to link N/A Links consolidated table to a selected chromatogram plot.
with
in the table.
in the table.
5.7.20.5 Results – Test Case Table

This table shows a summary of the system suitability test and Intelligent Run Control results of all injections in the current
sequence. An unlimited number of columns can be created, and each column can show any variable from section 7.
5.7.20.5.1 Filter By Case

Chromeleon 7

Filter By Case Type SST Case Displays only system suitability test cases in the report table.
Unconditional Case Displays only unconditional test cases in the report table.
Both Displays both system suitability test cases and unconditional
test cases in the report table.
5.7.20.5.2 Filter Results

Filter Test Results Show only executed test cases Limits display to only executed tests.
Include detailed results for peaks Displays the results of the peaks and aggregated injections in
and injections used for computing a separate line.
the statistic result

Grouping Options Group by test case Groups the report by test cases.
Group by injection Groups the report by injections.

the categories detailed in sections 7.1, 7.2 and 7.7
5.7.20.6 Results – MS Raw Spectra

This report table creates a list of the mass spectral peaks for the indicated chromatographic peak. The table consists of the
absolute and relative abundances for each of the detected mass fragments (m/z).
The following properties can be defined in the report:
5.7.20.6.1 Spectra
Interactive spectrum Displays the data of the currently selected spectrum.

Chromeleon 7
Peak spectrum Displays the spectrum data of a selected peak. Click the down arrow to specify the
criterion by which the peak is selected. The following criteria are available:
- by number
- by name
- by component table number
- by group
- ISTD (Internal Standard)
- by reference peak
- by SLS hit
- by condition
- by retention time
- by greatest area
- by greatest height
Spectrum of a fixed Retention Time (or bunched over Displays data for a spectrum with a specific retention time or a retention time
a time range) range. Type the appropriate retention time or time range in the min box.
Spectrum of a fixed Scan Number (or bunched over a Displays data for a spectrum with a specific scan number or a range of numbers.
number range) Enter the appropriate number or range in the min box.
5.7.20.6.2 MS Filter
Filter Filter definition to obtain data that match the specified filter settings.
5.7.20.6.3 Baseline Correction
No baseline correction No baseline correction is performed.
Use settings of processing method Baseline correction settings of the current processing method is used.
5.7.20.6.4 Noise Reduction
Use settings of processing method Use noise reduction settings defined in the processing method.
Do not reduce noise Does not exclude mass peaks from the plot based on their intensity values.
Relative Threshold, removes all masses below a Removes mass peaks from the plot that have an intensity below a specified
relative intensity of threshold value entered (in %) in the box.
Fixed Threshold Include only a specified number of mass peaks with the greatest intensities.
5.7.20.7 Results – Frame Table

This table is designed to show results of non-targeted MS processing. A limited number of columns can be created – one
column for each variable listed in section 7.37. The details in this table change, depending on which injection is being
viewed.
5.7.20.7.1 Frame Filter

See section 5.5.4.1 for details on use
5.7.20.7.2 Sort Options

Sort the report table according to the <List of Frame variables> Sorts the report table according to the user-selected Frame
evaluation of this formula variable. If disabled, the frame table is sorted by Frame ID

Chromeleon 7

all categories detailed in section 7.37.
5.7.20.8 Results - NTMS Processing Parameters Table

The NTMS Processing Parameters table shows the parameter values that were used to process each individual injection.
The entries shown are parameters that were defined in the processing method, but which were subject to change based on
the actual data for that injection.
This is a static table, with no customization properties.
5.7.20.9 Results – Tentative Identification Table

This table is designed to show results of tentatively identified peaks.

all categories detailed in section 7.37.

Chromeleon 7

Select the chromatogram plot to link N/A Links consolidated table to a selected chromatogram plot.
with
in the table.
5.7.20.10 Results - IPD Component Results Table

The Component Results pane displays a nested table of the protein deconvolution results.
5.7.20.10.1Filter

Display Individual When enabled, a sub-table will be added for each row to display individual injection results
Injections (Multiconsensus results only)
Charges When enabled, a sub-table will be added for each row to display individual charge state results
Components Match XXX of the ALL is equivalent to the AND logical operator. Finds injections with variable values that match all of
following rules the criteria specified in the rules that are assigned the AND logical operator.
ANY is equivalent to the OR logical operator. Finds injections with variable values that match any of
the criteria specified in the rules that are assigned the OR logical operator.
Variable Selects an intact protein deconvolution variable from the list.
Comparison Select the operator to be used for comparing variable values:
operator = (is equal to)
< (is less than)
> (is greater than)
is between
is not between
is during previous
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Injections Match XXX of the ALL is equivalent to the AND logical operator. Finds injections with variable values that match all of
following rules the criteria specified in the rules that are assigned the AND logical operator.

Chromeleon 7

< (is less than)
> (is greater than)
is between
is not between
is during previous
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
Charge Match XXX of the ALL is equivalent to the AND logical operator. Finds injections with variable values that match all of
States following rules the criteria specified in the rules that are assigned the AND logical operator.
< (is less than)
> (is greater than)
is between
is not between
is during previous
contains
does not contain
starts with
does not start with
ends with
does not end with
is any
is not any
is empty
is not empty
5.7.20.10.2Sort Options

Chromeleon 7
Sort the report table according to the Sorts the table according to the user defined formula (this can be based on any variable from the
evaluation of this formula Intact Protein Deconvolution in section 7).
Ignore case when comparing text results.
5.7.20.10.3Report Column

formula. This formula can be based only upon report variables
from the Intact Protein Deconvolution category detailed in
section 7.
5.7.20.11 Results - IPD Processing Parameters Table

The IPD Processing Parameters table shows the parameter values that were used to process each individual injection. The
entries shown are parameters that were defined in the processing method, but which were subject to change based on the
actual data for that injection.
This is a static table, with no customization properties.
5.7.20.12 Processing Method – Component Table

This table shows the component table defined in the processing method. An unlimited number of columns can be created,
and each column can show any variable from section 7. The details in this table can change if different chromatograms are
selected and the appropriate variables are displayed in the table.
Sort the report table according to the Sorts the table according to the user defined formula (this can be based on any variable in section
evaluation of this formula 7).
5.7.20.12.2Filter Components
Show only components with Limits table to only show specific channel for which you want to show the results in the report.
channel

Chromeleon 7

results.
channel.
defined here.
5.7.20.12.4Header Rows
5.7.20.13 Processing method – Peak Group Table

This report table shows the peak groups as defined in the processing method. An unlimited number of columns can be
created, and each column can show any variable from section 7.
The following properties can be defined for the report: The following properties can be defined for the report:
5.7.20.13.2Filter Peak Groups
Show only peak groups with Limits table to only display the peak groups that are assigned to the specified channel.
channel
Group Type Selection Controls which peak groups should appear in the report table depending on their corresponding
group type. Possible values are
Show all groups – all peak groups
Show only timed groups – only peak groups of group type ‘Timed Group’
Show only named groups – only peak groups of group type ‘Named Group’

Chromeleon 7

results.
channel.
defined here.
5.7.20.13.5Peak Group Results using the Peak Results / Calibration Category

The report table can also be used to report peak group evaluation results. For this purpose the formulas of the peak report
and calibration category (see 7.10 and 7.11 for details) are evaluated in a dedicated way, e.g. the formula peak.area will
return the sum of all areas of all peaks in the currently selected chromatogram belonging to the peak group. Such a group-
evaluation of peak-formulas is only available in this report table! Not all peak formulas provide a reasonable value for the
corresponding peak group. There is also the group evaluation property (Calibration, Reporting, None), which limits the
usage of peak-formulas, e.g. for group evaluation ‘None’, there is no peak-formula evaluation at all. Below is a list of valid
peak-formulas and their corresponding evaluations in this context, i.e. as a report column in a peak group result table.
Peak Formula Group Evaluation ‘Calibration’ Group Evaluation ‚Reporting‘

peak.amount The area/height of the peak group Sum of all amount values of all peaks which belong to the
peak.groupAmount is evaluated against the peak peak group are added together.
group calibration. The resulting
value is multiplied with the Factor-
value of the peak group record.
peak.amount_deviation The deviation of peak.amount vs. Sum of all amount_deviation values of all peaks which belong
the reference peak group amount to the peak group.
peak.area Returns the area of the peak Same as for Group-Evaluation ‘Calibration’.
peak.groupArea group, i.e. the sum of all area
values of all peaks which belong to
the peak group.
peak.calCoefficient and other Specific result of the group N/A
calibration relevant peak formulas calibration as calCoefficient,
calMode, calPointFx, etc.
peak.concentration The peak.amount value for the Similar to peak.amount all peak.concentration values of peaks
peak group (see above) divided by which belong to the peak group are added together.
the injection volume.

Chromeleon 7
Peak Formula Group Evaluation ‘Calibration’ Group Evaluation ‚Reporting‘

peak.height Returns the height of the peak Same as for Group-Evaluation ‘Calibration’.
peak.groupHeight group, i.e. the sum of all height
values of all peaks which belong to
the peak group.
peak.rel_amount Returns the relative amount where Returns the relative amount where the groupAmount (see
the groupAmount (see above) is above) as the nominator relative value.
the nominator of the relative value.
peak.rel_area Returns the relative amount where Same as for Group Evaluation ‘Calibration’.
the groupArea (see above) is the
nominator relative value.
peak.rel_height Returns the relative amount where Same as for Group Evaluation ‘Calibration’.
the groupHeight (see above) is the
nominator relative value.
For all “relative value” formulas above the reference value (denominator) depends on the corresponding parameter setting. For ‘All peaks of
the same group’ the corresponding values (Amount, Area, and Height) of all peaks which belong to the same peak group are added
together. In 7.2.9 you can also select a fixed group via ‘Fixed component or group’ and the corresponding group name. In this case the
groupAmount of the specified group is the reference value.
peak.name Returns the name of the peak Same as for Group Evaluation ‘Calibration’.
group which is Identical to the
peakGroup.name variable (see
7.29). This formula is also valid for
Group Evaluation ‘None’.
peak.group Returns the list of all assigned Same as for Group Evaluation ‘Calibration’.
named groups to the peak group
which is Identical to the
peakGroup.group variable (see
7.29). This formula is also valid for
Group Evaluation ‘None’.
Peak group results are also available in other report tables as Integration, Summary and Consolidated Report Tables. The
following peak-formulas return group relevant results:
Peak Formula Function

peak.name If an unidentified peak belongs to a timed group, peak.name returns the name of
this timed group. If such a peaks belongs to multiple timed groups, the name of
timed group with the smallest start time value is returned.
peak.group Returns the list of all named groups (possibly separated by list separator) where
the peak belongs to.
peak.groupAmount Returns the peak.groupAmount value as described in the previous table for the
peak group where the peak belongs to. If a peak belongs to more than one peak
group, the group amount of the first assigned peak group (lexicographic order) is
returned.
peak.groupArea Returns the peak.groupArea value as described in the previous table for the peak
group where the peak belongs to. If a peak belongs to more than one peak group,
the group area of the first assigned peak group (lexicographic order) is returned.
peak.groupHeight Returns the peak.groupHeight value as described in the previous table for the peak
group where the peak belongs to. If a peak belongs to more than one peak group,
the group height of the first assigned peak group (lexicographic order) is returned.
peak.rel_amount Similar to the “relative” peak formulas in the table above but now using the single
peak.rel_area peak amount, area or height values as the nominator. The reference value
(denominator) for the option ‘All peaks of the same group’ comes always from the
peak.rel_height first peak group to which the peak is assigned to (lexicographic order).
5.7.20.14 Processing Method – Detection Settings Table

This table shows the detection parameters defined in the processing method. This table contains no report columns and
cannot be modified. Note that this table does not show the global Cobra settings. These must be added as individual
variables (see section 7.27).

Chromeleon 7
5.7.20.15 Processing Method – Calibration History Table

This table is designed to show results based on the calibration type i.e. depending on which chromatogram the table is
printed out for and which calibration mode is selected the results will change. For example, if a bracketed calibration mode is
used the values in this table will depend on whether the table is printed for a sample in the first bracket or in the second
bracket. An unlimited number of columns can be created, and each column can show any variable from those detailed in
section 5.8.
5.7.20.15.1Grouping Options

Sort the report table according to Default order for injections Sorts the table according to injection number.
Evaluation of this formula Peaks are grouped by the user-defined formula.
group
results
Use Chromeleon 6 sort order Uses the sort order used in Chromeleon 6

results.
channel.
defined here.
Component Defines from which component the report column displays
peak results.
Selected Component: Displays values of currently selected
component.
Fixed Component: Displays values of the component as
defined here.
Component Row Defines content of Component header row.

Chromeleon 7
Component Displays an additional component header row.
5.7.20.15.4SmartLink

Select the chromatogram plot to link N/A Links calibration history table to a selected chromatogram
with plot.
5.7.20.16 Processing Method – SST and IRC Table

This table contains the Intelligent Run Control (IRC) configuration of the test cases defined on the SST/IRC tab page of the
Processing Method Editor.
5.7.20.16.1Filter By Case

Filter By Case Type SST Case Displays only system suitability test cases in the report table.
Unconditional Case Displays only unconditional test cases in the report table.
Both Displays both system suitability test cases and unconditional
test cases in the report table.
5.7.20.17 Processing Method – MS Detection Settings

This table shows the MS detection parameters defined in the processing method. This table contains no report columns.
5.7.20.17.1Display Settings

Show detection settings of N/A Defines which MS detection settings to show.
All Settings Displays all MS detection settings.
Processing Method Displays MS detection settings of a specific processing
method.
Selected Component Displays MS detection settings of the currently selected
component.
Fixed Component Displays MS detection settings of the component as specified
here.
5.7.20.18 Processing Method – Peptide Table

Upon import of a Pinpoint workbook, the Peptide Table will be populated which is primarily read-only. The user has the
ability to delete an isotope of a peptide but cannot re-add deleted peptide isotopes.
5.7.20.18.1 Sort Options
5.7.20.18.2Filter Peptides

Chromeleon 7
Show only components with Limits table to only show specific channel for which you want to show the results in the report.
channel

results.
channel.
defined here.
5.7.20.19 Instrument Method – Overview

This table contains general information about the instrument method as displayed on the Overview page of the Instrument
Method Editor. This table contains no report columns and cannot be modified.
5.7.20.20 Instrument method – Script

This table shows all the commands from the instrument method used for the injection. This table contains no report columns
and cannot be modified.
5.7.20.21 Instrument Method – MS Instrument Method (XRaw)

This table contains all the conditions from the MS Instrument Method used for the injection. This table contains no report
columns and cannot be modified.
5.7.20.22 Instrument Method – MS Tune Report

When MS data is acquired, the current Tune data is stored along with the dataset. Inserting an MS Tune Report into a report
sheet creates a table of the MS tune parameters used to acquire the data. The raw file data can contain multiple sets of
tunes.

Chromeleon 7
Show all sets Displays the data of all tune sets in the Xcalibur raw file.
Show set number A set number can be entered to display the data of the specified tune data set.
5.7.20.23 Instrument Method – Smart Startup / Shutdown / Standby Settings

This table contains the conditions defined for a Smart Startup, Smart Shutdown or Smart Standby procedure. This table
contains no report columns and cannot be modified.
5.7.20.24 Instrument Method – Extended

This table contains miscellaneous method information, such as Inverse Gradient information or embedded third-party
methods (for example, an Agilent ICF or Waters Acquity method). This table contains no report columns and cannot be
modified.
5.7.20.25 Status and Audit – Audit Trail Table

This table shows the audit trail and changes depending on which chromatogram is selected / printed. This table contains no
report columns. The following properties can be defined for the report table:
5.7.20.25.1Filter & Day Time

Filter Audit Level Defines the level of messages shown in the audit trail:
•Normal
•Advanced
•Expert
•Errors and Warnings
Show run Displays run audit trail entries.
Show preconditions Displays preconditions audit trail entries.
Day Time Format Defines the date and time formatting.
Show day time Displays day and time information.
Device Show device Displays device information.
5.7.20.26 Status and Audit – Data Audit Trail

This table shows the data audit trail depending on which object is defined. The following properties can be defined for the
report table:
5.7.20.26.1Filter

Object Type N/A Filters data audit trail table to defined object.
Current sequence Shows data audit trail of current sequence.
Current injection Shows data audit trail of current injection.
Current chromatogram Shows data audit trail of current chromatogram.
Current processing method Shows data audit trail of current processing method.
Current instrument method Shows data audit trail of current instrument method.
Current report template Shows data audit trail of current report template.
Time Restrictions Show all Shows all data audit trail entries.
Show data audit trail of recent Shows audit trail entries from the recent defined number of
days/weeks/months/years.
Show data audit trail from Shows data audit trail entries from defined date to the next
defined date.
5.7.20.26.2Sort Order

Chromeleon 7

Sort Order N/A Sorts data audit trail entries by Data/Time.
Ascending Sorts data audit trail entries by ascending data/time.
Descending Sorts data audit trail entries by descending data/time.

the categories detailed in sections 7.1, 7.2 and 7.7.
5.7.20.27 Status and Audit – Chromeleon 6 History Table

This table shows the Chromeleon 6 history only. The following properties can be defined for the report table:
5.7.20.27.1History Objects

Show Chromeleon 6 History of current injection Displays all modifications regarding the current injection.
current sequence Displays all modifications of all objects that are included in the
current sequence.
Current report template Displays all modifications of the current report definition file
(RDF).
current injection including Displays all modifications that may affect the quantification of
quantification the current injection.
current sequence including Displays all modifications that may affect the quantification of
quantification the current sequence.
fixed object Displays all modifications of a single object which can be

chosen. Objects can either be files, injections, sequences, or
directories.
Show also history of contents option to display modifications
of subdirectories, injections, or files contained.
5.7.20.27.2Time Restrictions

Time Restrictions Show all Shows all entries with no time restriction.
Show Chromeleon 6 history of Shows entries from the recent defined number of
recent days/weeks/months/years.
Show Chromeleon 6 history from Shows entries from defined date to the next defined date.
5.7.20.27.3Users

Chromeleon 7

Show Chromeleon 6 history of All users Shows Chromeleon 6 history of all users.
Selected users Shows Chromeleon 6 history of the selected users you can
select in the Users field.
All but selected users Shows Chromeleon 6 history of all user(s) except those
selected in the Users field.
5.7.20.27.4Operations

Operations to show N/A Defines operations to be displayed in the Chromeleon 6
History report.
General Contains general operations to select; Created, Created
(Save As), Changed, Copied, Moved, Deleted, Renamed,
Overwrite, Deleted Content.
Chromatogram Contains modifications affecting the chromatogram to select;
Save manipulations, Delete manipulations, Saved manual
peak identification, Deleted all manual peak identifications,
Saved results, Saved calibration.
Datasource & Directory Contains modifications affecting the datasource and the
Modifications directory; Disabled history mode, Enabled history mode –
comments required, Enabled history mode – no comments
required, Locked, Unlocked, Changed user access, Sample
GUID column created, Changed datasource protection,
Changed user-defined columns, Changed datasource
availability, Changed availability of sample status “Multiple”.
Batch Contains modifications affecting the batch; Started batch,
Finished batch, Aborted batch, Started diagnostics, Finished
diagnostics.
Miscellaneous Contains different modifications; Batch report, Export,
Changed sign requirements, Restored from Backup and
Verified, Failed to execute signed program, Saved to Backup,
Restored from Backup, Signed, Removed signature.
5.7.20.27.5Sort Order
History entry sorting Define how history entries are organized. The following variables are available under Sort by:
•Time
•Operator
•Operation
•Name
•Object Path
•Version
•Comment
Results of Sort by can then be further sorted by Ascending or Descending options.
Two variables can be combined using ‘Then by’: All variables under Sort by, except those previously
selected, can be used. Results can then be further sorted by Ascending or Descending options.
History detail sorting Define how history details are organized. The following variables are available under Sort by:
•Detail Number
•Detail Object
•Detail Column
•Detail Old Value
•Detail New Value
•Detail Comment
Results of Sort by can then be further sorted by Ascending or Descending options.
Two variables can be combined using ‘Then by’.All variables under Sort by, except those previously
selected, can be used. Results can then be further sorted by Ascending or Descending options.

Chromeleon 7

the categories detailed in sections 7.1, 7.2 and 7.7.
5.7.20.28 Status and Audit – MS Device Information

This table shows device-specific information about the mass spectrometer used for data acquisition, such as device name,
hardware and firmware version used. This table contains no report columns and cannot be modified.
5.7.20.29 Status and Audit – MS Status Log

When MS data is acquired, the current MS instrument status information is stored along with the dataset. Inserting an MS
Status Log into a report sheet creates a table of the MS instrument status parameters during the injection.
5.7.20.29.1Status Log Of
Status Log Number Displays information for a definable status log number.
Retention Time Displays the status log for a definable retention time.
Component Displays the status information from the scan at apex for a specific component using either Selected
Component or a Fixed Component.
5.7.20.30 Fractionation – Fraction Table

This table shows the fractions collected during the selected injection. An unlimited number of columns can be created, and
each column can show any variable from section 7.
5.7.20.30.1Filter Fractions
Show fractions of Shows fractions of the selected channel, all channels or a specific channel.


Chromeleon 7

results.
channel.
defined here.

Select the chromatogram plot to link N/A Links fraction table to a selected chromatogram plot.
with
in the table.
in the table.
5.7.20.31 Fractionation – Tube Table

This table shows the tubes of the currently selected injection. An unlimited number of columns can be created, and each
column can show any variable from section 7.
5.7.20.31.1Filter Tubes
Show tubes outside of fractions Includes any tubes collected outside of fractions in the table.


Chromeleon 7

results.
channel.
defined here.

Select the chromatogram plot to link N/A Links fraction table to a selected chromatogram plot.
with
in the table.
in the table.
5.7.21 Chromeleon Report Variables

Chromeleon report variables can be inserted into any cell of the report sheet. See section 7 for details of variables available.
5.7.21.1 Mathematical Operators

The following mathematical operators can be used in any numeric report variable or report table column:
• + (Add) • * (multiply) • / (divide)
• - (Minus) • ^n (exponentiation) • - a (unary minus (negative
value))
Report variables can be multiplied, etc. by numbers or by other numeric report variables.

Chromeleon 7
5.7.22 Spreadsheet Formula

It is possible to enter Spreadsheet formula directly into Chromeleon report definition files. The following formulae are
supported:
• ABS • EXACT • MATCH • SIGN
• ACOS • EXP • MAX • SIN
• ACOSH • FACT • MID • SINH
• ADDRESS • FALSE • MIDB • SLOPE
• AND • FIND • MIN • SQRT
• ASC • FINDB • MINUTE • STDEV
• ASIN • FIXED • MOD • STDEVP
• ASINH • FLOOR • MONTH • SUBSTITUTE
• ATAN • HLOOKUP • N • SUM
• ATAN2 • HOUR • NA • SUMIF
• ATANH • IF • NOT • SUMSQ
• AVERAGE • INDEX • NOW • T
• CEILING • INDIRECT • ODD • TAN
• CHAR • INT • OFFSET • TANH
• CHOOSE • INTERCEPT • OR • TEXT
• CLEAN • ISBLANK • PI • TIME
• CODE • ISERR • PRODUCT • TIMEVALUE
• COLUMN • ISERROR • PROPER • TODAY
• COLUMNS • ISLOGICAL • RAND • TRIM
• CONCATENATE • ISNA • REPLACE • TRUE
• CORREL • ISNONTEXT • REPLACEB • TRUNC
• COS • ISNUMBER • REPT • TYPE
• COSH • ISREF • RIGHT • UPPER
• COUNT • ISTEXT • RIGHTB • VALUE
• COUNTA • LEFT • ROUND • VAR
• COUNTIF • LEFTB • ROUNDDOWN • VARP
• DATE • LEN • ROUNDUP • VLOOKUP
• DATEVALUE • LENB • ROW • WEEKDAY
• DAY • LN • ROWS • YEAR
• DAYS360 • LOG • SEARCH
• DBCS • LOG10 • SEARCHB
• ERRORTYPE • LOOKUP • SECOND
• EVEN • LOWER
• Print & Export Settings
The Print & Export settings define which pages of the report will be printed for which samples. It also defines the export
options for the report. These options can be modified by the user when batch reporting the sequence. The following options
are available:
5.7.22.1 Print Settings

The Print Settings Dialog box is divided in two sections:
• Printer: select printer to print this report

Chromeleon 7
• Select Sheets to be printed: Select which sheets will be printed when. For each sheet of the report the following
print options are available:

Print N/A When tagged the sheet is printed under the
conditions set in the conditions column.
Condition Each Injection The sheet is printed for each injection.
Blank The sheet is printed for all blank injections.
Matrix The sheet is printed for all matrix injections.
Spiked The sheet is printed for all spiked injections.
Unspiked The sheet is printed for all unspiked injections.
Calibration Standard The sheet is printed for all calibration standard
injections.
Check Standard The sheet is printed for all check standard
injections.
Unknown The sheet is printed for all unknown injections.
First Injection Prints the sheet for the first injection in the
sequence.
Last Injection Prints the sheet for the last injection in the
sequence.
Last Injection in a list of cal. standards Prints the sheet for the last injection in a list of
standards.
More Conditions Prints the sheet under user defined conditions.
For details see table below.
Create an electronic report option generates an electronic report that contains the results of the current sequence.
The More condition options are:
More conditions Any field from the sequence table – Restricts when the sheet is printed based on
including user defined columns comparing the selected variable with a user-
defined value and using the following logical
arguments:
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Starts with
Doesn’t start with
Ends with
Doesn’t end with
Contains
Doesn’t contain
Is empty
Is not empty
Is any
Is not any
Multiple conditions can be added.
5.7.22.2 Export Settings

Destination Path Parent Folder The location for the export file. Can either be a fixed text value
or based on a Chromeleon report variable. All the variables
listed in section 7 can be used.

Chromeleon 7

Sub Folder The formula for the directory for the export file. Can either be a
fixed text value or based on a Chromeleon report variable. All
the variables listed in section 7 can be used.
Export Formats & Filenames Text format (Results) (.txt) Exports the results as an ASCII file.
Text format (Raw Data) (.txt) Exports the raw data as an ASCII file.
Excel file format (.xls) Exports the sequence as an Excel file.
PDF file format (.pdf) Exports the sequence as an Acrobat file.
GAML file format (*. gaml) Exports the sequence to Generalized Analytical Markup
Language file format.
AnDI/NetCDF file format (*.cdf) Exports the sequence to Analytical Data Interchange file
format.
Raw file format (.raw) Exports MS raw data to the raw data file format, which can be
opened in applications such as Xcalibur.
Chromeleon data file format Exports the sequence to a Chromeleon data file format.
(*.cmbx)
Allotrope Data File Format (*.adf) Exports the sequence to an Allotrope XML file
External Program Call external program If activated, launches an external program during the batch
report/export.
Notifications Enable Notifications If activated, email notifications (as configured in the Export
Notifications Settings window) will be sent during the batch
export.
For all export formats chosen it is possible to define a file name. This can either be a fixed text value or based on a
Chromeleon report variable. All the variables listed in section 7 can be used. Choices for which sheets are exported are the
same as for the print settings (see 5.7.22.1).
5.7.22.2.1 External Program

This section allows the conditions under which external program will be run, to be defined. The following options are
available:

Program N/A Name and location of file to be opened.
Arguments N/A User defined formula based on Chromeleon variables. All
variables detailed in section 7 can be used).
Execution Options Offline Batch If activated allows the external program to be run if the batch is
processed offline.
Online Batch If activated allows the external program to be run if the batch is
processed online.
Do Not Execute The external program is not run.
Execute after each injection The external program is executed after each sample.
Execute under certain conditions The external program is executed under certain conditions.
The conditions available are the same as for the print
conditions (see section 5.7.22.1).
Wait until External Program N/A The next client action is started only after the external program
Terminates stops running.
Wait up to x minutes N/A The start of the next client action is delayed for at least x
minutes. Enter the desired maximum delay time in the entry
field. If the external program stops running before the delay
time has elapsed, the next client action will automatically start
immediately.
Do not wait for external program to N/A With this option, the execution of the next client action does not
terminate wait for the external program to stop running.
5.7.22.2.2 Export Notification Settings

This window allows the conditions under which email notifications will be sent during exporting to be defined. The following

Chromeleon 7

Send notification email when Mail recipient Email address(es) of person(s) to receive email notification
sequence finishes exporting when the export is produced.
Include the user who created the N/A If enabled, the user who created the sequence will be notified,
sequence in addition to the other recipients specified above
Include the user who last modified N/A If enabled, the user who last modified the sequence will be
the sequence notified, in addition to the other recipients specified above
5.7.23 Page Setup

The following options are available for the page setup:
5.7.23.1 Page
Option Sub Option Description

Orientation Portrait Prints the sheet with portrait orientation.
Landscape Prints the sheet with landscape orientation.
Scaling Scale to: The scale of the printout (fixed %).
Fit to If activated this option ensures that the printout is fitted to the
selected number of pages (wide and tall). Note: This option will
shrink the size of the text and graphics to the selected number
of pages but will not expand the size.
5.7.23.2 Margins

Margins N/A Defines the Top, Bottom, Left and Right margins as well as the
margins for the Header and Footer.
Center on page Horizontally Centers the printout horizontally
Vertically Centers the printout vertically.
5.7.23.3 Header/Footer
Headers and footers can contain text and specific format codes. The syntax is compatible with Microsoft Excel. Observe the
order of the single entries.
Codes can be entered into the Left, Center, and Right areas of the header and footer.
The default font is Arial 10. A different font can only be defined after the header and/or footer alignment has been defined.
The new font can be defined as follows:
• &B: Bold • &U: Underline • &"fontname": Uses the specified font
• &I: Italic • &S: Strikeout • &nn: Uses the specified font size
Finally, the following parameters can be defined:
• &A Prints the current sheet name

• &D Prints the current date
• &T Prints the current time
• &F Prints the Report Template file name
• &P Prints the page number
• &P+Number Prints the following page number: current page + entered number. For example: &P+4 prints
page 16 if the current page is page 12.
• && Prints an ampersand
• &N Prints the total number of pages in the document
In addition to the pre-defined variables above, you can enter variables pertaining to Chromeleon. These variables must be
enclosed in braces. Example:

Chromeleon 7
Operator: {gen.loggedOnUser} , Instrument: {seq.instrument} , Sequence:{seq.name} Page &P of &N &D

This example produces the following header or footer:
Operator: cmadmin, Instrument: HPLC, Sequence: Calibration Page 1 of 12 4/6/2011
5.7.23.4 Sheet

Print Gridlines Prints grid lines between the cells
Row Headings Prints the row headings.
Column Headings Prints the column headings
Black and White Prints any colored objects in black and white.
Page Order Top to Bottom Defines the order in which the information is printed if the
printout required more than 1 page.
Left to Right
5.7.23.5 Print Area

When the report contains more data than required to print, the print area can be set. The print area defines the area of the
report sheet that will be printed. After setting a print area it is possible to release it again.
5.7.23.6 Print Titles

When a table is large it can extend on multiple pages (horizontally or vertically). In these cases, it is useful to repeat specific
rows or columns as titles at the top or on the left of every printed page. This option is available in the Page Setup group on
the Page Layout ribbon tab. The following options are available:
Set Print Titles Set the selected rows or columns as print titles.
Release Print Titles Releases the set print titles.
5.7.24 Autorepeat Areas

It is often useful to repeat the output of reports for other channels, injections, components, and peaks, other than the
currently selected. In Chromeleon, you can automatically repeat the output of reports for:
• Each injection of a sequence or selection
• Each component in a component table or the current chromatogram
• Each peak of an injection
• Each channel of an injection
Up to two object types may be specified for autopreating. If two object types are specified, then autorepeat occurs in a nested fashion. For
example, if one specifies autorepeat by injection and then by component, the order of the reported data will be:
The data from all injections for the first component
The data from all injections for the second component
And so on
Note: Only one autorepeat area can be defined on each sheet in a report definition file.
5.7.24.1 General Settings

(Level 1) None Do not autorepeat the selected area.
Repeat the report objects inside the Channels Autorepeat the selected area for certain channels.
autorepeat are for:
Injections Autorepeat the selected area for certain injections.
Components Autorepeat the selected area for certain components.
Peaks Autorepeat the selected area for certain peaks.
Grouping Items per group Limits the number of items shown in one object.

Chromeleon 7

Sort by Can define a report variable to sort the objects. All the
variables listed in section 7 can be used.
(Level 2) None Do not autorepeat the selected area.
Repeat the report objects inside the Channels * Autorepeat the selected area for certain channels.
autorepeat are for:
Injections * Autorepeat the selected area for certain injections.
Components * Autorepeat the selected area for certain components.
Peaks * Autorepeat the selected area for certain peaks.
Grouping Items per group Limits the number of items shown in one object.
Sort by Can define a report variable to sort the objects. All the
variables listed in section 7 can be used.
Insert x line(s) after each channel N/A Select this check box to add x empty lines after each channel
(where x can be set).
Insert page break after each N/A Select this check box to output the selected area for each
channel channel on a separate sheet of paper.
Don’t split report tables across N/A The content of an auto-repeated table is printed on one page
multiple pages unless the content of the table is too large to fit completely on
one page, in which case a page break is inserted, and the
content is continued on subsequent pages.
* If an object type is specified for Level 1 autorepeat, then it will be excluded as a sub-option for Level 2
5.7.24.2 Channel Settings
All Evaluation Channels The entire page will be reported for the first Evaluation Channel. The selected area
will be repeated for all other evaluation channels.
These Channels Lists all channels. The entire page will be reported for the first channel enabled in
the list. The selected area will be repeated for all other channels enabled in the list.
Channel(s) of same detector as the current channel The entire page will be reported for the first channel of the current detector. The
selected area will be repeated for all other channels of this detector.
Channel(s) of detector Lists all detectors. The entire page will be reported for the first channel of the
detectors enabled in the list. The selected area will be repeated for all other
channels of these detectors.
5.7.24.3 Component Settings

All Components N/A The entire page will be reported for the first component in the
component table of the Processing Method. The selected area
will be repeated for all other components in the component
table.
These Components N/A Lists all components. The entire page will be reported for the
first component in the list. The selected area will be repeated
for all other components enabled in the list.

Chromeleon 7

Components that match the ALL (Any field from the sequence Restrict the data points shown based on comparing the
following conditions table – including user defined selected variable with a user-defined value and using the
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
columns]
5.7.24.4 Injection Settings

Custom Conditions Only include injections that match Displays injections that fulfill a certain condition.
the following conditions

Chromeleon 7

Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
columns]
Stop repeat after each x injections N/A Select check box to stop the auto-repeated reporting after a
certain number of injections (where x is the number of
injections).
5.7.24.5 Peak Settings

Repeat Peaks Identified Peaks Shows all peaks that have been identified.

Chromeleon 7
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
columns]
5.7.25 Protection
Sheets can be protected in Chromeleon 7. Once the protection is enabled it is possible to lock/unlock specific cells and
graphics (see Figure 50).
Figure 50: Sheet Protection Options
5.7.26 Check for Errors

The entire report can be checked for errors, using the check for errors button in the Home ribbon tab of the report designer.
The following results are available:
Errors in report Lists all error types that were found during the error check, as well as the number of errors for each
error type.
Check Again Re-runs the error check.
Location Shows the location (sheet name and cell number) of the selected error.
Formula Shows the formula that contains the error.
Error Details Gives details on the error.
5.7.27 Custom Formulas

The Custom Formulas Manager can be opened using the button in the Home ribbon tab of the report designer. The
following actions and information are available:

Chromeleon 7
Add Opens custom formulas editor (see section 3.1.4)
Remove Deletes the custom formula from the sequence
Edit Opens custom formulas editor (see section 3.1.4)
Used in Shows which objects within the sequence use the custom formula
Location Shows the location (sheet name and cell number) of the selected error.
Formula Shows the details of the custom formula
Description Shows the description of the custom formula

Chromeleon 7
5.8 Electronic Reports

Electronic reports are a snapshot of the sequence results that are captured electronically and stored in the sequence.
Figure 51 shows a typical electronic report.
Figure 51: Report Template in the Chromatography Studio
5.8.1 Creation Settings

The settings are divided into two sections:
Choose a report template and channel: select report template and channel
Choose the sheets and define the conditions: Select which sheets will be printed when. For each sheet of the report the

Include N/A When tagged the sheet is printed under the
conditions set in the conditions column.
Condition Each Injection The sheet is printed for each injection.
Blank The sheet is printed for all blank injections.
Matrix The sheet is printed for all matrix injections.
Spiked The sheet is printed for all spiked injections.
Unspiked The sheet is printed for all unspiked injections.
Calibration Standard The sheet is printed for all calibration standard
injections.
Check Standard The sheet is printed for all check standard

Chromeleon 7
injections.
Unknown The sheet is printed for all unknown injections.
First Injection Prints the sheet for the first injection in the
sequence.
Last Injection Prints the sheet for the last injection in the
sequence.
Last Injection in a list of cal. standards Prints the sheet for the last injection in a list of
standards.
More Conditions Prints the sheet under user defined conditions.
For details see table below.
The More condition options are:
More conditions Any field from the sequence table – Restricts when the sheet is printed based on
including user defined columns comparing the selected variable with a user-
defined value and using the following logical
arguments:
Is equal to (=)
Is larger than (>)
Is smaller than (<)
Is like
Is not like
Is between
Is not between
contains
does not contain
Starts with
Does not start with
Ends with
Does not end with
Is any
Is not any
Is empty
Is not empty
Is during previous
Multiple conditions can be added.
5.9 Spectral Library

Spectral libraries serve for identifying unknown substances. Spectra can be saved in spectra libraries and later compared to
the spectrum of the unknown substance.
Apart from absorption values, each spectrum in a library contains various ID data fields that are freely editable by the user
and that facilitate spectra searches. The following fields are available:
Field Description
Spectrum Thumbnail image of the spectrum.
Name Shows the name under which the substance is included in the spectra library.
ID Shows the short ID that is assigned to the spectrum. Use this column to save several
spectra under the same substance name in a spectra library. The Ids, such as
consecutive numbers, then distinguish the spectra ID.
#Extrema Shows the number of extreme values in the spectrum determined by the system.
Select a column entry to change the number.
Solvents Shows the solvent in which the spectrum was recorded. Select a column entry to edit.
Comment Use this column to document details on the saved spectrum.

Chromeleon 7
Field Description
WL-Range Indicates the wavelength range of the recorded spectrum.
WL-Resolution Shows the Bandwidth with which the spectrum was recorded.
Ret.Time [min] Indicates the retention time at which the spectrum was extracted from a peak.
Ret. Index Indicates the Retention Index of the substance.
Acq.Step Indicates the Step with which the underlying 3D Field was recorded.
Detector Indicates the detector with which the spectrum was recorded. The name is taken from
the Server Configuration.
Detector Serial No. Indicates the serial number of the detector from the Server Configuration.
Instrument Indicates the name of the instrument with which the spectrum was recorded.
Sequence Indicates the name of the sequence in which the spectrum was recorded.
Injection Shows the name of the sample from which the extracted spectrum is taken.
Acq. Date/Time Shows the date and time at which the spectrum or the underlying 3D field was
originally acquired.
Instrument Method Shows the name of the instrument method, which was used for generating the
underlying chromatogram.
Extract Date/Time Shows the data and time at which the spectrum was extracted and saved.
Extract Operator Shows the name of the user who extracted the spectrum and saved it to the spectra
library.
Spectra can be copied into the library via options provided in the ribbon. All data associated with the spectrum (e.g.
Retention time, Detector, etc.) is copied along with the spectrum.
5.10 MS Spectral Library

Spectral libraries serve for identifying unknown substances. Mass spectra can be saved in custom NIST format mass
spectral libraries and later compared to the spectrum of the unknown substances. Apart from spectra, each entry is
identified by chemical name or peak number and retention time.

Chromeleon 7
5.11 Data Audit Trail

A data audit trail records all changes made to any data object in a Chromeleon Data Vault with versioning enabled. Each
object has a separate data audit trail. The audit trail is recorded automatically and cannot be disabled by users (including
system administrators).
Figure 52 above shows the data audit trail of a folder.
Figure 52: Data Audit Trail

The data audit trail offers the following top-level functions:
Reload Reloads the data audit trail from the Data Vault.
Report Creates a report of the data audit trail.
Compare Compares the changes between any two selected versions of an item, or changes
made in one version if only one entry is selected.
Restore Restores the selected version of an object. The new version will not overwrite the
current version but is a version on its own and is only persisted when saved by the
user.
Studio Opens a read-only Chromatography Studio window of the currently selected object
and the corresponding version. If the object (e.g. Processing Method) is located in a
sequence the corresponding sequence version is opened in the read-only window.
Include Subfolders When enabled, versions of objects in subfolders are included in the data audit trail.
From <date> to <date> Allows to filter the list to changes made in the given time range.
Filtering Provides a filtering option for each of the columns in the data audit trail.
Grouping Allows the data audit trail to be grouped by any of the columns available.
Find Next Finds the next data audit trail entry that meets the search criteria.
Find Previous Finds the previous data audit trail entry that meets the search criteria.
Finally, the data audit trail offers some functionality that can be accessed by right clicking on any one of the data audit trail
entries:
Compare Compares the changes between any two selected versions of an item, or changes
made in one version if only one entry is selected.
Restore Restores the selected version of an object. The new version will not overwrite the
current version but is a version on its own and is only persisted when saved by the
user.
Studio Opens a read-only Chromatography Studio window of the currently selected object
and the corresponding version. If the object (e.g. Processing Method) is located in
a sequence the corresponding sequence version is opened in the read-only
window.

Chromeleon 7
Show Data Audit Trail… Shows the data audit trail of the selected data object in a new data audit trail
window.

Chromeleon 7
5.12 Injection Audit Trail

The audit trail records a log of all information that was recorded in the Instrument Audit Trail for a specific injection. The audit
trail is recorded automatically and cannot be disabled by users (including system administrators).
Figure 53 above shows some of the details commonly recorded in the audit trail.
Figure 53: Injection Audit Trail

The injection audit trail offers the following top-level functions:
Copy Copies selected audit trail entries to the clipboard.
Print Prints the audit trail.
Display Offers 4 options:
•All: Shows all audit trail entries
•Run Only: Shows audit trail entries related to events that occur while a
sequence is running
•Preconditions only: Shows audit trail entries related to system status prior to
an injection
•Errors and Warnings: Shows only errors and warnings
Level Offers 3 options:
Normal: Only shows audit trail entries for normal user level.
Advanced: Shows audit trail entries for normal and advanced user level.
Expert: Shows audit trail entries up to expert user level.
Next Injection Shows audit trail entries for the next injection.
Previous Injection Shows audit trail entries for the previous injection.
Find Next Finds the next audit trail entry that meets the search criteria.
Find Previous Finds the previous audit trail entry that meets the search criteria.
The audit trail also offers some functionality that can be accessed by right clicking on any one of the column headers:
Table Columns Allows definition of which columns should be displayed and in which order.
Fill Last Column Ensures that the last column is extended to fill an empty space.
Show Group Area Activates the grouping option.
Show Tool Strip Shows/hides the tool strip.

Chromeleon 7
Finally, the audit trail offers some functionality that can be accessed by right clicking on any one of the audit trail entries:
Select All Selects all audit trail entries.
Scale Columns to Fit Page Ensures that the audit trail columns are sized to fit the screen view.
Print Preview Offers a print preview.

Chromeleon 7
6 Versioning
Chromeleon 7 supports full versioning of the following objects:
• Data Vaults
• Folders
• Injections
• Injection Queries
• Instrument Audit Trails
• Chromatogram
• Sequences
• Instrument Method
• Processing Method
• Report Template
• Electronic Reports
• Spectral Libraries
• View Settings
Full copies of each object are retained when modifications or deletions are performed, allowing for prior version to be
restored. In addition, each time an object is modified or deleted, details on the creation, modification, and deletion of files is
recorded in the data audit trail. The following information is recorded:
Information Description
Number Master version number. For example, if changes are made to 4 separate objects within a sequence the
master version number will be increased by 4, even though the version number for the associated objects
is only increased by 1.
Name Name of the object
Type Object type
Version Version number of the object
Date/Time Date/time of the action
Operator User id of the operator performing the action
Operation Type of operation performed
Comment User entered comment
Any two versions of an object can also be compared, and the comparison tool shows all changes from one version to
another. As all versions are stored, it is also possible to restore a previous version of an object.

Chromeleon 7
7 Chromeleon Variables
This section details all the variables that Chromeleon can report.
7.1 Global Functions
Absolute Value Returns the absolute value of a given number. The number can be defined by a Chromeleon report
variable.
Convert to Text Converts the variable to text.
Create Time The Create Time function constructs an object for representing the given date and (optional) time. This
function is required for formulas where a date is used as a constant.
Exponential Function Returns the exponential function of a given value.
Find Position of Text The Find Position of Text function returns the starting position of the text to be found within the text to
search in, starting at the defined start position.
If Allows use of an If command that reports different values based on the following criteria: if(<condition>,
<truevalue>,<falsevalue>).
IsError Reports a value of False if the entered variable does not return an error, and a value of True if it does
report an error.
Logarithm Returns the logarithm function of a given value. The base can be defined as a parameter.
Natural Logarithm Returns the natural logarithm function of a given value.
Round Value Rounds a given number to the specified number of digits. The number can be defined by a Chromeleon
report variable.
Select Left Text Selects text from a text variable based on the defined number of characters from the right of the text.
Select Middle Text Selects text from a text variable based on the starting character and a defined length.
Select Right Text Selects text from a text variable based on the defined number of characters from the left of the text.
7.2 General

Computer Name N/A The PC name.
Current Printer N/A Printer used for printing the report.
Current Time N/A The current date and time.
Logged On User Full Name Full name of the logged-on user.
Job Title Job title of the logged-on user.
User Name User id of the logged-on user.
My Documents Folder N/A Returns the path of the "My Documents" folder in Windows. If you export
a report, the "My Documents" folder will be the default location.
Report Mode N/A Indicates whether the report was generated automatically or manually
Serial Number N/A The installation serial number (taken from the Chromeleon license key,
locally or from the Chromeleon Domain Controller).
Version Number N/A The Chromeleon version installed on the PC.
7.3 Sequence

Approve Comment N/A Comment that was added in the Approve Signature dialog box during the
Electronic Signature process.

Chromeleon 7

Approve Date & Time Format date/time as text The date and time when the sequence results were approved during the
Electronic Signature process can have the following formats:
•Default date/time format
•ISO 8601 date/time
•Localized long date
•Localized short date
•Time offset only
•Time with seconds and time offset
•Time with time offset
Time in universal The time in coordinated universal time standard format.
coordinated time
Time offset in hours The time offset from your local time based on the Windows settings of
your local computer (including any daylight-savings time adjustments that
apply)
Time using local time zone The conversion of date and time to your local time zone with the following
formats:
•Format date/time as text
•Time offset only
•Time offset in hours
Approve Operator Full Name Full name of the user who approved the sequence results during the
Job Title Job title of the user who approved the sequence results during the
User Name User id of the user who approved the sequence results during the
Comment N/A Sequence comment.
Created by qualification N/A
Creation Date & Time Format date/time as text The date and time the sequence was created can have the following
formats:
•Time offset only
coordinated time
your local computer (including any daylight savings time adjustments that
apply)

Chromeleon 7

formats:
•Time offset only
Creation Operator Full Name Full name of the operator who created the sequence.
Job Title Job title of the operator who created the sequence.
User Name User id of the operator who created the sequence.
Custom Variable N/A The value entered for a custom variable.
Data Vault N/A Name of the corresponding data vault.
Default Channel N/A The default channel
Default Report Template N/A The default report template.
Default View Settings N/A The default view settings.
Directory N/A Directory in which the sequence is stored.
Displaying Imported Results N/A Indicates whether the results were imported or not.
eWorkflow Name N/A The name of the eWorkflow that was used to create the sequence.
Imported Data N/A Indicates whether the data was imported or not
Instrument N/A Assigned instrument for the sequence.
Last Update Date & Time Format date/time as text The date and time the last changes made to the sequence were saved
can have the following formats:
•Time offset only
coordinated time
apply)
formats:
•Time offset only
Last Update Operator Full Name Full name of the user who last saved changes to the sequence.
Job Title Job title of the user who last saved changes to the sequence.

Chromeleon 7

User Name User id of the user who last saved changes to the sequence.
Name N/A Sequence name.
Number of Injections N/A Number of injections in the sequence.
Review Comment N/A Comment that was added in the Review Signature dialog box during the
Review Date & Time Format date/time as text The date and time when the sequence results were reviewed during the
•Time offset only
coordinated time
apply)
formats:
•Time offset only
Review Operator Full Name Full name of the user who reviewed the sequence results during the
Job Title Job title of the user who reviewed the sequence results during the
User Name User id of the user who reviewed the sequence results during the
Select Injection Select by number Selects a given injection for which to display a chosen result. All
parameters from section Injections (0) can be chosen.
Select by name
Signature Status N/A The current Electronic Signature status of the sequence.
Signature Steps N/A The Electronic Signature steps (Submit, Review or Approve) that are
defined for the sequence.
Submit Comment N/A Comment that was added in the Submit Signature dialog box during the
Submit Date & Time Format date/time as text The date and time when the sequence results were submitted during the
•Time offset only
coordinated time

Chromeleon 7

apply)
formats:
•Time offset only
Submit Operator Full Name Full name of the user who submitted the sequence results during the
Job Title Job title of the user who submitted the sequence results during the
User Name User id of the user who submitted the sequence results during the
Version Comment Comment for this version.
Computer Name Name of the computer on which this version was created.
Data Vault Name of the data vault.
Date & Time Date and time when the version was created. The same sub functions as
for other date & time variables are available
•Time in universal coordinated time
•Time using local time zone
•Time offset only
Number Version number.
Operator Information about the user who created the version. The same sub
functions as for other operator variables are available. These are
Full Name, Job Title and User Name.

Chromeleon 7
7.4 Injection

Adducts N/A Displays the positive and negative adducts defined for the injection. This
can be in a single line or in multi-line format
Adduct Masses N/A Displays the target masses adjusted for the positive and negative adducts
defined for the injection. This can be in a single line or in multi-line format
Auto Dilution Ratio N/A Returns the value of dilution ratio which is how much the sample amount
will be reduced in the re-injection.
Calculated Mass Custom Variable Selects an injection custom variable to calculate a mass from
Fixed Formula User-defined molecular formula or peptide sequence to calculate mass
from
Peptide Defines formula source as a peptide sequence – no post-translational
modifications are allowed
Chemical Formula Defines formula source as a molecular formula
Positive Defines the molecule as positively charged
Negative Defines the molecule as negatively charged
Charge Defines the charge state of the molecule
Adduct Selects the adduct gain or loss
Chemical Formula and Adducts N/A Displays the chemical formula for the target masses, including the positive
and negative adducts defined for the injection. This can be in a single line
or in multi-line format
Chemical Formula and Adduct N/A Displays the masses of the positive and negative adducts defined for the
Masses injection. This can be in a single line or in multi-line format
Comment N/A The injection comment
Custom Variable N/A The value entered for a custom variable.
Dilution N/A The injection dilution factor.
Evaluate Context The location context of the custom variable (Injection, Sequence,
Component, or Unidentified Peak Group).
Custom Variable List of variables from the selected context only.
GUID N/A Displays globally unique identifier assigned to given injection.
Inject Time Format date/time as text The date and time the injection data acquisition started can have the
following formats:
•Time offset only
coordinated time
apply)

Chromeleon 7

formats:
• Default date/time format
• ISO 8601 date/time
• Localized long date
• Localized short date
• Time offset only
• Time with seconds and time offset
• Time with time offset
• Time offset in hours
Instrument Method N/A The instrument method used for the injection.
IntStd N/A The injection Internal Standard amount.
Level N/A The calibration leve
Level Check N/A The result of level tolerance checks for all applicable components in a
single injection.
Lock Status N/A Lock status of the injection.
Lock Version Comment Comment for this version.
•Time offset only
Name N/A The injection name
Number N/A The injection number
Number of re-injections N/A Displays number of re-injections for injection in injection list.
Position N/A The injection position
ProcessingMethod N/A The processing method used for the injection.
Reference Retention Time N/A The injection number and injection name of the retention time standard
Standard referenced by the current injection.
Relative Position N/A Specifies a value for the Relative Position (in the range -9999 to 9999)
Replicate ID N/A The injection Replicate ID.
Retention Time Standard Error N/A The returned error if the injection is an invalid retention time standard.
Retention Time Standard N/A The status (Valid, Invalid, or n.a.) of a retention time standard.
Status

Chromeleon 7

Select Chromatogram N/A Parameter from the selected chromatogram. Some variables in this
category depend on the type of detectors connected during the data
acquisition.
The options for select chromatogram are:
•Use preferred channel of sequence
•Use fixed channel
All parameters from section Chromatogram (7.8) can be chosen.
Spike group N/A The spike group for the injection.
Status N/A Displays status of injection
Test Case Overall Result N/A The result of all test cases for the current injection (system suitability test
(SST) cases only).
Test Case Specific Result Select by number Selects a given test case either by name or number and the results of a
specific test case can be reported by selecting a variable from the Test
Select by name Case Result category.
Type N/A The injection type
•Time offset only
Volume N/A The injection volume.
Weight N/A The injection weight
7.5 Audit Trail

The audit trail records all actions executed to an instrument. Depending on the connected instrumentation, hundreds of
Audit Trail variables are available. The lists below show only those variables that are applicable to an UltiMate 3000 HPG-
3200RS pump or a Ultimate 3000 DAD-3000(RS) detector.
7.5.1 HPG-3200RS Pump Audit Trail Variables

Maximum Flow Ramp Down The maximum flow ramp down.
Maximum Flow Ramp Down The maximum flow ramp-up.
Lower Limit The lower pressure limit
Upper Limit The upper pressure limit

Chromeleon 7
Equate (%A, %B) Name of eluent component A, B.
Type (%A, %B) Type of eluent component A, B.
Flow The pump flow rate.
%A, %B The percentage of the respective component in the eluent.
Curve The curve of the gradient.
7.5.2 DAD-3000(RS)
Max. Wavelength (3DFIELD) The maximum wavelength of the 3D Field.
Min. Wavelength (3DFIELD) The minimum wavelength of the 3D Field.
Bunch Width The bunch width of the diode group.
Response Time The response time of the detector.
Data Collection Rate The data collection rate.
Demo File Name The demo file name used when running in evaluation mode.
Wavelength The wavelength setting of a single acquisition channel.
Bandwidth The bandwidth setting of a single acquisition channel.
Ref Wavelength (UV) The reference wavelength of a single acquisition channel.
Ref Bandwidth (UV) Reference Bandwidth of a single acquisition channel.
Ref Wavelength (3D Field) The reference wavelength of the 3D Field.
Ref Bandwidth (3D Field) Reference Bandwidth of the 3D Field.
7.6 Preconditions
Depending on the connected instrumentation, thousands of Preconditions variables exist. They allow you to display in the
Audit Trails the device settings existing immediately before a sample run. (For more information about the Audit Trails see
section 4.4).
7.7 Data Audit Trail

Additional Information N/A Displays additional information regarding the data audit trail
record.
Comment N/A Displays the data audit trail comment which the user has put in.
Date/Time N/A Date and time stamp of modification.
Object Name N/A Name of the modified object.
Object Version N/A Version of the modified object.
Operation N/A Modification to the object.
Operator Full Name Full name of the user who performed the modification.
Job Title Job Title of the user who the modification.
User Name User id of the user who the modification.
Type N/A Type of the modified object.
7.8 Chromatogram
Some variables in this category depend on the type of detectors connected during the data acquisition. The tables below
show the standard variables that are always available and the variables that are available when a UVD 340 is used for data
acquisition.

Chromeleon 7
7.8.1 Standard Variables

Auto Noise (Cobra) Actual noise Indicates the noise level at a given retention time if the auto noise
option is selected.
Noise level used to search Indicates the noise level used for searching the baseline segment
Noise level of rank Indicates the noise level at a given rank in percent (e.g. 50%
returns the median noise level)
Baseline Threshold (Cobra) N/A Indicates the threshold for automatic detection of baseline
segments in the Cobra peak detection at the start-time of the
chromatogram or at a given retention time.
Channel N/A User defined name of the data channel.
Count Peaks If… N/A Counts peaks based on a user-defined condition.
Curvature (Cobra) N/A Indicates the value of the 2nd derivative of the chromatogram for
a given retention time.
Curvature Noise (Cobra) N/A The noise in the 2nd derivative at the start-time of the
chromatogram or a given retention time.
Delay Time N/A The delay time between two detectors.

Detection Algorithm N/A The name of the detection algorithm (Chromeleon 6, Cobra,
Genesis, or ICIS) that is currently used for the current
chromatogram.
Detector N/A Name of the detector used to acquire the channel.
Effective Min. Peak Area (Cobra) N/A Indicates the minimum peak area that is applied by the Cobra
peak detection at the start-time of the chromatogram or a given
retention time.
Effective Min. Peak Height (Cobra) N/A Indicates the minimum peak area that is applied by the Cobra
peak detection at the start-time of the chromatogram or a given
retention time.
Effective Smoothing Width (Cobra) N/A Indicates the smoothing width value the Cobra peak detection is
applying at a given retention time of the chromatogram.
End Time (relative to Inject Time) N/A Chromatogram end time [min].
Evaluate Context The location context of the custom variable (Injection, Sequence,
Component, or Unidentified Peak Group).
Fluorescence Spectrum Retention Time Information about a fluorescence spectrum at a certain retention
time from the FL Spectrum category (see section 7.13).
Filter Information about a fluorescence spectrum, filtered for scan type,
photomultiplier or other options (see section 5.7.9.6) from the FL
Spectrum category (see section 7.13).
Import Type N/A Import format type.
Injection Specific XIC Detection Full Name Full name of the user who last modified the injection specific XIC
Operator detection parameter for the chromatogram.
Job Title Job Title of the user who last modified the injection specific XIC
detection parameter for the chromatogram.
User Name User id of the user who last modified the injection specific XIC
detection parameter for the chromatogram..
Injection Specific XIC Detection Format date/time as text The date and time of the last modification of the injection specific
Time XIC detection parameter for the chromatogram can have the
following formats:

Chromeleon 7

Time in universal coordinated The time in coordinated universal time standard format.
time
Time offset in hours The time offset from your local time based on the Windows
settings of your local computer (including any daylight savings
time adjustments that apply)
Time using local time zone The conversion of date and time to your local time zone with the
following formats:
• Format date/time as text
Injection Specific XIC Detection? N/A Indicated if the chromatogram has been processing with enabled
injection specific XIC detection parameters.
Manipulated? N/A Indicates if the chromatogram has been manually manipulated or
not.
Mass Detected N/A Indicates if the target mass specified for the injection (adjusted for
adducts) was detected in the specified filter
Mass Spectrum Spectrum Selection Spectrums selected based upon spectrum of a fixed Retention
Time (or bunched over a time range) or spectrum of a fixed Scan
Number (or bunched over a number range)
Spectrum Filter Specifies the acquisition filter from which the chromatogram is
extracted.
Baseline Correction Information about a mass spectrum, with or without baseline
correction.
Noise Reduction Information about a mass spectrum with or without noise
reduction. When applying noise reduction, a Relative Threshold,
removes all masses below a relative intensity of base peak or a
Fixed Threshold, which limits spectra to only a number of largest
mass intensities for a peak.
Metadata Compute value of metadata Returns additional signal information, such as the polarity, source
voltage, or filter number of a mass channel.
Modification Operator Full Name Full name of the user who last modified the chromatogram.
Job Title Job Title of the user who last modified the chromatogram.
User Name User id of the user who last modified the chromatogram.
Modification Time Format date/time as text The date and time of the last modification can have the following
formats:
time

Chromeleon 7

following formats:
MS Signal Extraction Parameter N/A All variables in section 7.9 become available.
Noise Determination Range End N/A Indicates the end time of the time range that is used by Cobra
Time (Cobra) peak detection to compute the peak and baseline thresholds.
Noise Determination Range Start N/A Indicates the start time of the time range that is used by Cobra
Time (Cobra) peak detection to compute the peak and baseline thresholds.
Number of Peaks N/A Total number of peaks in the chromatogram.
Peak Threshold (Cobra) N/A Indicates the minimum curvature for peaks that is used for peak
detection with Cobra at the start-time of the chromatogram or a
given retention time.
Sample Rate Minimum rate Minimum sample rate at which raw data points were recorded.
Maximum Rate Maximum sample rate at which raw data points were recorded.
Average rate Average sample rate at which raw data points were recorded.
Sample Step Minimum Step Minimum step.
Maximum Step Maximum step.
Average Step. Average step.
Select Peak By name Selects peak by peak name.
By number Selects peak by peak number in the chromatogram.
By component table number Selects peak by peak number in the peak table.
By group Selects peak by peak group.
ISTD (Internal Standard) Selects the internal standard peak.
Reference peak Selects the reference peak.
By SLS-hit Selects peak by hits in the spectra library.
By condition Selects peak based on a user-defined condition.
By retention time Selects peaks based on retention time settings e.g. retention time
and window.
By greatest area Selects peak by area.
By greatest height Selects peak by height.
Signal Description N/A Key parameters for the recorded signal.
Signal Drift N/A The signal drift for the noise determination range that is used for
peak determination or over a user defined time segment.
Signal Noise N/A The signal noise for the noise determination range that is used for
peak determination or over a user defined time segment.
Signal Statistic Computed statistic The type of statistical value computed from signal data which can
be either minimum signal value, maximum signal value or
average signal value.
Time range The time range for computing the statistical value either of the
entire chromatogram or over a user defined time segment.
Signal Unit N/A The units the signal is reported in e.g. mAU*min.
Signal Value N/A The signal value of the chromatogram at a given retention time.

Chromeleon 7

Slope (Cobra) N/A The slope i.e. the value of the 1st derivative of the chromatogram
for a given retention time.
Start Time (relative to Inject Time) N/A Chromatogram start time [min].
Sum Peak Results If… N/A Adds together user defined peak results based on a user-defined
variable or condition.
UV Spectrum Retention Time Information about a UV spectrum at a certain retention time from
the UV Spectrum category (see section 7.17).
Baseline Correction Information about a UV spectrum, with or without baseline
correction, from the UV Spectrum category (see section 7.17).
Date & Time Date and time when the version was created. The same sub
functions as for other date & time variables are available
• Time in universal coordinated time
• Time using local time zone
Operator Information about the user who created the version. The same
sub functions as for other operator variables are available. These
are
7.9 MS Signal Extraction Parameters
Auto Filter The text definition of the scan filter.
End Time The ending retention time of the extraction.
Evaluation Type The type of extracted ion chromatogram in MS data (quantitation peak or confirming
peak).
Mass Ranges Mass ranges used for extraction.
Number of Smoothing Points The number of points used for smoothing, if smoothing is enabled.
Smoothing Algorithm The localized name of the smoothing algorithm.
Start Time The starting retention time of the extraction.
Trace Type The localized name of the extracted ion chromatogram type.
7.10 Peak Results

In order to show results for these variables a peak from the component table must be selected. Also, the variable can be
configured to show the data from the current channel selected by the user or from a specified channel.

Chromeleon 7

Amount N/A The calculated peak amount
Calibration curve for amount When using the Standard Addition calibration mode, you can
calibration (Standard Addition choose whether the amount is calculated by using the
only) calibration curve with or without offset.
Amount correction for spiked When using the Standard Addition calibration mode, you can
samples (Standard Addition only) choose whether the amount is calculated with or without
subtracting the reference amount.
Amount Deviation Absolute in amount units The difference between the calculated amount and the
expected amount.
Relative in % of the expected The relative difference (%) between the calculated amount and
amount the expected amount.
Area Full Time Range of Peak The peak area ([signal]*min) of the peak.
Custom Time Range from x min to The peak area ([signal]*min) for a specified retention time
y min range.
Asymmetry (EP, AIA, Statistical N/A The asymmetry of the peak, based on EP/USP, AIA or
Moments) Statistical Moments
Baseline Value at Peak End N/A The baseline signal value at the peak end.
Baseline Value at Peak retention N/A The baseline signal value at the peak retention time.
Baseline Value at Peak Start N/A The baseline signal value at the peak start.
CE Area N/A The CE peak area (area/retention time)
Concentration N/A The peak concentration i.e. the peak amount divided by the
injection volume of the sample.
Detection Code at Peak End N/A The detection code at peak end.
Detection Code at Peak Start N/A The detection code at peak start.
Evaluate Context The location context of the custom variable (Injection,
Sequence, Component, or Unidentified Peak Group).
Group N/A The name(s) of the named peak group(s) the peak belongs to.
Group Amount N/A The calculated amount of the respective peak group.
Group Area N/A The total area of all peaks in the respective peak group.
Group Height N/A The total height of all peaks in the respective peak group.
Height N/A The peak height ([signal]) of the peak.
K’ N/A The K’ value of the peak. Can be computed against a fixed
dead time, or the dead time defined in the processing method.
Left Width The baseline level The left width of the peak at the baseline.
5 % height over the baseline The left width of the peak at 5 % height over the baseline.
Custom The left width at a user defined % height over the baseline.

Chromeleon 7

Level Check N/A The pass or fail result for components at levels where the
tolerance % is defined.
Level Tolerance High Amount N/A The maximum allowable concentration for the peak to pass
tolerance test.
Level Tolerance High Response N/A The maximum allowable signal for the peak to pass tolerance
test.
Level Tolerance Low Amount N/A The minimum allowable concentration for the peak to pass
tolerance test.
Level Tolerance Low Response N/A The minimum allowable signal for the peak to pass tolerance
test.
Manipulated? N/A Indicates whether the peak has been manually modified or not.
Manually Assigned N/A Indicates whether the peak name has been manually assigned
or not.
Name N/A The peak name.
Number N/A The peak number.
Peak Start Time N/A The time at which the peak integration starts.
Peak Stop Time N/A The time at which the peak integration ends.
Peak to Valley Ratio N/A The ratio for a peak in an unresolved peak group, which is an
indicator of the quality of peak separation.
The ratios are calculated based on USP (= United States
Pharmacopeia) and PharmEU standards:
Relative Amount All Identified Peaks The amount portion of the peak relative to all identified peaks in
the chromatogram.
All peaks of the same group The amount portion of the peak relative to all peaks in the
respective group.
The corresponding ISTD The amount portion of the peak relative to the corresponding
component ISTD component.
The corresponding reference The amount portion of the peak relative to the corresponding
component Reference component.
Fixed component The amount portion of the peak relative to the user selected
component.
Relative Area All detected peaks The relative area of the peak as a percentage of all peaks in the
chromatogram.
All identified peaks The relative area of the peak as a percentage of all identified
peaks in the chromatogram.
All peaks of the same group The relative area of the peak as a percentage of all peaks in the
respective peak group.
The corresponding ISTD The relative area of the peak as a percentage of the
component corresponding ISTD component.
The corresponding reference The relative area of the peak as a percentage of the
component corresponding reference component.
Fixed component The relative area of the peak as a percentage of the user
selected component.
Multiply values before computing Multiply the peak area values with the returned values of a
the relative result with formula before the results are calculated
Relative CE Area All detected peaks The relative CE area of the peak as a percentage of all peaks in
the chromatogram.
All identified peaks The relative CE area of the peak as a percentage of all
identified peaks in the chromatogram.
All peaks of the same group The relative CE area of the peak as a percentage of all peaks in
the respective peak group.

Chromeleon 7

The corresponding ISTD The relative CE area of the peak as a percentage of the
The corresponding reference The relative CE area of the peak as a percentage of the
Fixed component The relative CE area of the peak as a percentage of the user
selected component.
Multiply values before computing Multiply the peak CE area values with the returned values of a
Relative Height All detected Peaks The relative height of the peak as a percentage of all peaks in
the chromatogram.
All identified Peaks The relative height of the peak as a percentage of all identified
peaks in the chromatogram.
All peaks of the same group The relative height of the peak as a percentage of all peaks in
the respective peak group.
The corresponding ISTD The relative height of the peak as a percentage of the
The corresponding reference The relative height of the peak as a percentage of the
Fixed component The relative height of the peak as a percentage of the user
selected component.
Multiply values before computing Multiply the peak height values with the returned values of a
Relative Retention Time First or used reference component The relative retention time of the peak relative to the reference
component or a selected component.
Fixed component
The relative retention time can be reported as a percentage
Reference component (CM6 value (%). This may be expressed with the following formula:
compatibility mode)
Convert to percentage
Resolution (EP, USP, Statistical Next main peak Resolution between the peak and the next main peak in the
Moments) chromatogram.
Previous main peak Resolution between the peak and the previous main peak in the
chromatogram.
Next identified peak Resolution between the peak and the next identified peak in the
chromatogram.
Previous identified peak Resolution between the peak and the previous identified peak
in the chromatogram.
Corresponding reference Resolution between the peak and the corresponding reference
component peak.
Corresponding internal standard Resolution between the peak and the corresponding ISTD
component peak.
Fixed component Resolution between the peak and a selected peak from the
component table in the quantification method.
Retention Deviation Absolute in minutes The deviation (in minutes) between the actual retention time
and the expected retention time.
Relative in % of the expected The relative deviation (%) between the actual retention time
retention time and the expected retention time.

Chromeleon 7

Retention Index Interpolation function type Determines the type of function used to calculate interpolation
(linear, quadratic, cubic, logarithmic). By default, Chromeleon
calculates the following linear retention index:
Wherein:
RI = Retention index (usually RI = 100, 200, 300 is entered)
S = Substance
Z = number of the marker
The following is true:
If the peak occurs before the first or behind the last marker
peak, and the Extrapolate check box is selected, the formula is
calculated for the first two and last two peaks, respectively.
Use detected retention times of Specifies which retention times Chromeleon uses for
calculating the retention index.
“Current injection” uses the retention times of the current
injection.
“Most recent injection with condition” uses the retention times of
the most recent injection that meets a certain condition.
If the “Include expected retention times for not detected
components” check box is activated, the expected retention
times of peaks that were not detected are excluded from
calculation.
The “Subtract dead time (Kovats Index)” check box provides
the Kovats Index if activated.
Extrapolate If the option “Extrapolate if the peak's retention time is outside
the retention time reference range” is deactivated, Chromeleon
excludes the retention times outside the specified retention time
reference range from extrapolation.
Retention Time Detected value The retention time (in minutes) of the peak.
Expected value The expected retention time (as defined in the quantification
method) of the peak.
At a given peak area % The retention time when the specified relative peak area is
reached.
Retention Window Width N/A The width of the retention window (as defined in the component
table of the processing method).
Right Width the baseline level (base width, The right width of the peak at the baseline.
default)
5 % height over the baseline The right width of the peak at 5 % height over the baseline.
Custom The right width at a user defined % height over the baseline.
Signal to Noise Ratio Injection for noise calculation Calculates noise from:
•Current injection
•Blank run injection of the corresponding processing
method
•Recent blank run in sequence
•Fixed injection
Method of noise calculation Calculates noise using:
Peak to peak (ASTM)
RMS

Chromeleon 7

Time range for noise calculation - Use x times the “variable y” equally around the peak
boundaries.
Options for variable y:
•Peak width at 50% height
•Base peak width
- Use a fixed time interval from x to y min
- Use n datapoints from retention time x
- Find the lowest noise range consisting of n datapoints
Signal Value at Peak End N/A The signal value at the peak end.
Signal value at Peak Retention N/A The signal value at the peak retention time.
Signal Value at Peak Start N/A The signal value at the peak start.
Skewness N/A The skewness of the peak.
SN Intermediate Results Injection for noise calculation Calculates noise from:
•Current injection
•Blank run injection of the corresponding processing
method
•Recent blank run in sequence
•Fixed injection
Method of noise calculation Calculates noise using:
Peak to peak (ASTM)
RMS
Time range for noise calculation - Use x times the “variable y” equally around the peak
boundaries.
Options for variable y:
•Peak width at 50% height
•Base peak width
- Use a fixed time interval from x to y min
- Use n datapoints from retention time x
- Find the lowest noise range consisting of n datapoints
Statistical Moments Zeroth moment The zero moment (peak area).
First moment The first moment (averaged retention time).
Second Moment The second moment (retention time variance).
Theoretical Plates (EP, USP, JP, N/A The number of theoretical plates for the peak.
Statistical Moments)
Type N/A Peak Type.
Note: If a peak has been manually integrated the “*” symbol is
appended to the peak type.
Width the baseline level (base width, The peak width at the baseline.
default)
5 % height over the baseline The peak width at 5 % height over the baseline.
Custom The peak width at a user defined % height over the baseline.
7.11 Peak Calibration

In order to show results for these variables a peak from component table must be selected. Also, the variable can be

Calibration Coefficient N/A Shows the relevant calibration coefficient for a user-defined
exponent e.g. 0 (zero) provides the intercept, 1 supplies the
slope, etc.

Chromeleon 7

Calibration Mode N/A The calibration mode used.
Calibration Point Status Current injection Returns the calibration point status for the current injection
(default). If the current injection is not involved in the
calibration, the entry reads n.a.
Minimum x-value Returns the calibration point status for the calibration point
with the minimum x-coordinate.
Maximum x-value Returns the calibration point status for the calibration point
with the maximum x-coordinate.
Minimum y-value Returns the calibration point status for the calibration point
with the minimum y-coordinate.
Maximum y-value Returns the calibration point status for the calibration point
with the maximum y-coordinate.
Number of calibration point Returns the calibration point status for a certain calibration
standard. The number is considered as consecutive number
regarding the list of all calibration standard injections.
Calibration Point Weight Current injection Returns the weight factor for the current injection (default). If
the current injection is not involved in the calibration, the entry
reads n.a.
Minimum x-value Returns the weight factor for the calibration point with the
minimum x-coordinate.
Maximum x-value Returns the weight factor for the calibration point with the
maximum x-coordinate.
Minimum y-value Returns the weight factor for the calibration point with the
minimum y-coordinate.
Maximum y-value Returns the weight factor for the calibration point with the
maximum y-coordinate.
Number of calibration point Returns the weight factor for a certain calibration standard.
The number is considered as consecutive number regarding
the list of all calibration standard injections.
Calibration Point X/Y Current injection Returns the calibration point x/y value for the current injection
(default). If the current injection is not involved in the
calibration, the entry reads n.a.
Minimum x-value Returns the calibration point x/y value for the calibration point
with the minimum x-coordinate.
Maximum x-value Returns the calibration point x/y value for the calibration point
with the maximum x-coordinate.
Minimum y-value Returns the calibration point x/y value for the calibration point
with the minimum y-coordinate.
Maximum y-value Returns the calibration point x/y value for the calibration point
with the maximum y-coordinate.
Number of calibration point Returns the calibration point x/y value for a certain calibration
standard. The number is considered as consecutive number
regarding the list of all calibration standard injections.
Calibration Type N/A The calibration type of the peak.
Coeff. of Determination N/A The coefficient of determination (R-square) value for the
calibration curve associated with the peak.
Correlation Coefficient N/A The linear correlation coefficient.
DOF-Adjusted Coeff. of N/A The coefficient of determination corrected by the degree of
Determination freedom.
Evaluation of Cal. Function for X Current injection Returns the value of the calibration function for the x-value of
the calibration point. If the current injection is not involved in
the calibration, the entry reads n.a.
Minimum x-value Returns the value of the calibration function for the x-value of
the calibration point with the minimum x-coordinate.
Maximum x-value Returns the value of the calibration function for the x-value of
the calibration point with the maximum x-coordinate.

Chromeleon 7

Minimum y-value Returns the value of the calibration function for the x-value of
the calibration point with the minimum y-coordinate.
Maximum y-value Returns the value of the calibration function for the x-value of
the calibration point with the maximum y-coordinate.
Number of calibration point Returns the value of the calibration function for the x-value of
a certain calibration standard. The number is considered as
consecutive number regarding the list of all calibration
standard injections.
Hubaux Vos Limit of Detection Upper prediction limit Select a probability of a true positive detection (equal to 1-α,
where α is the probability of a false positive detection). For
example, an upper prediction interval of 99% corresponds to
an α value of 1%.
Lower prediction limit Select a probability of a true negative detection (equal to 1-β,
where β is the probability of a false negative detection). For
example, a lower prediction interval of 95% corresponds to a
β value of 5%.
Lower Confidence Limit (From Smallest calibration level The lower confidence limit of the calibration curve at the
Processing Method, 95, 97.5, 99, smallest calibration level.
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The lower confidence limit of the calibration curve at the
greatest calibration level.
Average of all calibration levels The lower confidence limit of the calibration curve at the
average of all calibration levels.
Reference amount (calibration and The lower confidence limit of the calibration curve at the
check standards \ QC Sample reference amount level.
only)
Computed amount The lower confidence limit of the calibration curve at the
computed amount.
Any fixed value: x The lower confidence limit of the calibration curve at the
specified amount (x)
Probability The probability (confidence level) that the specified values are
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
99.995% or can be set to be read from processing method
selected in the Low. Conf. Prob or Up. Conf. Prob column of
Lower Prediction Limit (From Smallest calibration level The lower prediction limit of the calibration curve at the
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The lower prediction limit of the calibration curve at the
Average of all calibration levels The lower prediction limit of the calibration curve at the
Reference amount (calibration and The lower prediction limit of the calibration curve at the
only)
Computed amount The lower prediction limit of the calibration curve at the
computed amount.
Any fixed value: x The lower prediction limit of the calibration curve at the
specified amount (x).
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
Number of Calibr. Points N/A The number of calibration points in the calibration curve
associated with the peak.
Number of disabled Calibr. Points N/A The number of disabled calibration points in the calibration
curve associated with the peak.
Reference Inject Volume N/A The reference inject volume selected.
Relative Standard Deviation N/A The relative standard deviation value for the calibration curve

Chromeleon 7

Relative Standard Error N/A The relative standard error value for the calibration curve
Residual of Calibr. Point X Current injection The difference between the expected Y value for the
calibration point and the actual Y value. If the current injection
is not involved in the calibration, the entry reads n.a.
Minimum x-value The difference between the expected Y value for the
calibration point with the minimum x-coordinate and the actual
Y value.
Maximum x-value The difference between the expected Y value for the
calibration point with the maximum x-coordinate and the
actual Y value.
Minimum y-value The difference between the expected Y value for the
calibration point with the minimum y-coordinate and the actual
Y value.
Maximum y-value The difference between the expected Y value for the
calibration point with the maximum y-coordinate and the
actual Y value.
Number of calibration point The difference between the expected Y value for a certain
calibration point with the minimum x-coordinate and the actual
Y value.
RF-Value (Amount/Area) N/A The reciprocal of the slope (c1) value i.e. the peak
amount/peak area.
Standard Deviation N/A The standard deviation value for the calibration curve
Upper Confidence Limit (From Smallest calibration level The upper confidence limit of the calibration curve at the
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The upper confidence limit of the calibration curve at the
Average of all calibration levels The upper confidence limit of the calibration curve at the
Reference amount (calibration and The upper confidence limit of the calibration curve at the
only)
Computed amount The upper confidence limit of the calibration curve at the
computed amount.
Any fixed value: x The upper confidence limit of the calibration curve at the
specified amount (x).
correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
Upper Prediction Limit (From Smallest calibration level The upper prediction limit of the calibration curve at the
99.5, 99.9, 99.95 or 99.995)
Greatest calibration level The upper prediction limit of the calibration curve at the
Average of all calibration levels The upper prediction limit of the calibration curve at the
Reference amount (calibration and The upper prediction limit of the calibration curve at the
only)
Computed amount The upper prediction limit of the calibration curve at the
computed amount.
Any fixed value: x The upper prediction limit of the calibration curve at the
specified amount (x)

Chromeleon 7

correct: 95%, 97.5%, 99%, 99.5%, 99.9%, 99.95%, and
Variance N/A The variance value for the calibration curve associated with
the peak.
Variance Coefficient N/A The variance coefficient value for the calibration curve
Weights N/A The Weights variable returns a text identifying the weighting
method that is defined in processing method.
7.12 Peak Purity and Identification

In order to show values for these variables a peak from the component table must be selected. Also, the variable can be
Composite Scoring All variables in section 7.13 become available.
Confirmation Chromatogram Chromatogram of corresponding confirmation ion. All variables in section 7.8.1
become available.
Confirmation Peak The number of the corresponding confirming peak. All variables in section 7.10
become available.
Fluorescence Spectrum All variables in section Error! Reference source not found. become available.
ISTD Chromatogram Chromatogram of the corresponding ISTD peak. All variables in section 7.8.1 become
available.
ISTD Peak ISTD peak. All variables in section 7.10 become available.
MSLS Hit Information about the matching mass spectra (hits) found
during MS library screening. All variables in section 7.15 become available.
Number of MSLS Hit The matching mass spectra (hits) found during MS library screening
Number of SLS hits The number of hits in the spectral library.
Peak Confirmation Ratio The peak confirmation ratio of a user definable number of component traces.
Peak Confirmation Result The peak confirmation result. Can be computed against all component traces, or a
user definable number of component traces.
Peak Mass Spectrum Information about the mass spectrum. All variables in section 7.16 become available.
Peak Purity Index The peak purity index of the peak.
Peak Purity Match Average peak purity match.
Peak Ratio Mean Value The mean value of the quotients of all (baseline-corrected) signal data point values (of
a peak) from the current and the first channel (in alphabetic order) of the same
detector that is not the current channel (for example, if UV_VIS_2 is the current
channel of a UV detector, UV_VIS_1 is used for the calculation).
Peak UV Spectrum All variables in section 7.17 become available.
Reference Spectrum Match The match factor with the reference spectra.
RSD Peak Purity Index The relative standard deviation of the peak purity index.
RSD Peak Purity Match The relative standard deviation of the peak purity match.
RSD Peak Ratio The relative standard deviation of the peak ratio mean value.
SLS Hit The rank of the match can be defined and all variables in section 7.18 become
available.
Tentative Identification All variables in section 7.19 become available.

Chromeleon 7
7.13 Composite Scoring (Peak Purity and Identification)
Variable Parameter Description

Amount Difference <Parameterless> Returns the difference as a percentage (%) in peak amount between
data obtained from 2 discrete detectors as defined by the processing
method.
<Channel Name> Returns the difference as a percentage (%) in peak amount between
data obtained from 2 discrete detectors with the reference channel
defined by the processing method and confirmation channel defined by
the parameter selection.
Composite Score Processing Method Overall composite scoring result based on results evaluated defined by
Amount ratio Composite scoring result based on evaluation of amount ratio
confirmation as defined by the processing method.
Isotopic Dot Product <Parameterless> Composite scoring result based on evaluation of isotopic dot product
between theoretical and observed isotope distributions of peptides.
Mass Accuracy <Peak Number> Composite scoring result of mass accuracy against an exact mass. The
parameterless report variable returns a result for the quantitation peak.
Otherwise, the variable returns mass accuracy for the designated
confirmation peak.
Peak Apex Alignment <Peak Number> Composite scoring result of peak apex alignment against the
quantitation peak.
7.14 FL Spectrum

Baseline Corrected N/A Returns whether Baseline Correction is enabled in the
Processing Method.
Baseline Correction Bunch Side Returns the baseline correction left/right bunch width for peak-
dependent baseline correction on the UV Spectra Settings
dialog box of the Processing Method Editor
Noise N/A The noise for the whole wavelength range of the spectrum.
Number of relative Extrema N/A The number of relative extrema of the spectrum.
Property Unit N/A Unit of meta data property of the spectrum.
Property Name Defines the property.
Property Value N/A Value of meta data property of the spectrum.
Property Name Defines the property.
Restrict Wavelength Range Use sub range from x nm to y nm Restricts wavelength range of spectrum considered for
calculations to entered values.
Retention Time N/A The retention time of the spectrum.
Scan Index N/A The peak purity index of the spectrum.
Scan Maximum N/A Indicates the upper limit of the wavelength range of the
reference spectra.
Scan Minimum N/A Indicates the lower limit of the wavelength range of the
reference spectra.
Scan Resolution N/A Indicates the optical resolution of the reference spectra.
Scan Unit N/A Indicates the unit of the scan axis.

Chromeleon 7

Scan Value Compute wavelength of the The scan value (usually the wavelength) of an absolute or
relative signal extremum.
Options are:
•absolute minimum
•absolute maximum
•greatest relative maximum
•second greatest relative maximum
•third greatest relative maximum
•fourth greatest relative maximum
•fifth greatest relative maximum
Signal Maximum N/A The maximum value on the signal axis.
Signal Minimum N/A The minimum value on the signal axis.
Signal Unit N/A Indicates the unit of the signal axis.
Signal Value Compute at wavelength The signal value for a selected scan value of the spectrum.
Statistical Moment N/A The first statistical moment for the spectrum.
7.15 Hit Mass Spectrum

CAS Number N/A Chemical Abstracts Service (CAS) registry number of the chemical
associated with the mass spectrum found during MS library screening.
Chemical Formula N/A The chemical formula of a mass spectrum found during MS library
screening.
Library Name N/A The name of the MS library in which the mass spectrum found during MS
library screening is stored.
Match Factor N/A The Match Factor for the hit mass spectrum and the mass spectrum
submitted for MS library screening.
Molecular Weight N/A The molecular weight of a mass spectrum found during MS library
screening.
Name N/A The chemical name of the mass spectrum found during MS library
screening.
Probability N/A The probability (in %) that a mass spectrum found during MS library
screening matches the spectrum submitted for screening.
Reverse Match Factor N/A The Reverse Match Factor of the hit mass spectrum and the mass
spectrum submitted for MS library screening.
Spectrum Data N/A It returns the mass or intensity of a peak in the mass spectrum found during
MS library screening. By default, the mass or intensity of the mass peak
with the greatest mass in the spectrum is reported.
7.16 Mass Spectrum

Intensity N/A The intensity of a peak in a mass spectrum. By default, the
intensity is reported for the mass peak with the greatest mass
in the spectrum.
Compute Intensity for the mass The intensity of the mass peak according to its relative rank in
peak with the ... the mass spectrum, based on either the peak's mass or its
intensity.
Compute Intensity for the mass Reports the intensity of a mass peak at a specific mass to
peak at ... charge ratio.
Mass N/A The mass of a peak in the mass spectrum found during MS
library screening according to its relative rank in the mass
spectrum, based on either the peak's mass or its intensity.

Chromeleon 7

Mass Range N/A Reports the extracted mass range.
Maximal Mass N/A Maximal mass of the spectrum mass range.
Minimal Mass N/A Minimal mass of the spectrum mass range.
Number of Data Points N/A Number of mass data points in the mass spectrum.
Relative Intensity N/A Relative intensity of a peak in the mass spectrum.
Resolution N/A Resolution of the peak in the mass spectrum.
Spectrum Type N/A Spectrum type of the mass
spectrum.
TIC N/A Total of intensities of the single peaks in the mass spectrum.
7.17 UV Spectrum

Baseline Corrected N/A Returns whether Baseline Correction is enabled in the
Processing Method.
Baseline Correction Bunch Side Returns the baseline correction left/right bunch width for peak-
dependent baseline correction on the UV Spectra Settings
dialog box of the Processing Method Editor
Noise N/A The noise for the whole wavelength range of the spectrum.
Number of relative Extrema N/A The number of relative extrema of the spectrum.
Restrict Wavelength Range Use sub range from x nm to y nm Restricts wavelength range of spectrum considered for
calculations to entered values.
Retention Time N/A The retention time of the spectrum.
Scan Index N/A The peak purity index of the spectrum.
Scan Maximum N/A Indicates the upper limit of the wavelength range of the
reference spectra.
Scan Minimum N/A Indicates the lower limit of the wavelength range of the
reference spectra.
Scan Resolution N/A Indicates the optical resolution of the reference spectra.
Scan Unit N/A Indicates the unit of the scan axis.
Scan Value Compute wavelength of the The scan value (usually the wavelength) of an absolute or
relative signal extremum.
Options are:
•absolute minimum
•absolute maximum
•greatest relative maximum
•second greatest relative maximum
•third greatest relative maximum
•fourth greatest relative maximum
•fifth greatest relative maximum
Signal Maximum N/A The maximum value on the signal axis.
Signal Minimum N/A The minimum value on the signal axis.
Signal Unit N/A Indicates the unit of the signal axis.
Signal Value Compute at wavelength The signal value for a selected scan value of the spectrum.
Statistical Moment N/A The first statistical moment for the spectrum.
7.18 Hit Spectrum

Chromeleon 7

Acquisition Step N/A The sample rate that was used to record the spectrum.
Comment N/A Comment of the hit spectrum.
Component Name N/A The peak name of the hit spectrum.
Data Acquisition Date/Time N/A Date and time the injection used to obtain the hit spectrum was acquired.
Detector Name N/A The name of the detector used to acquire the hit spectrum.
Detector Serial Number N/A The serial number of the detector used to acquire the hit spectrum.
Extract Date/Time Format date/time as The date and time when the spectrum was extracted can have the following
text formats:
•Time offset only
coordinated time
Time offset in hours The time offset from your local time based on the Windows settings of your
local computer (including any daylight savings time adjustments that apply)
Time using local time The conversion of date and time to your local time zone with the following
zone formats:
•Time offset only
Extract User Name N/A The user id of the operator who extracted the hit spectrum.
ID N/A The unique identifier (ID) of the spectrum.
Injection N/A Provides details of the injection used to extract the hit spectra. Allows use of
any variable from the Injections category (see 0).
Injection Name N/A The name of the injection from which the spectrum was extracted.
Injection URL N/A Provides the URL of the injection used to extract the hit spectrum.
Instrument N/A The instrument used to obtain the hit spectrum.
Instrument Method N/A The name of the instrument method used to run the injection that was used
to obtain the hit spectrum.
Library Name N/A The name of the spectral library containing the hit spectrum.
Library Record N/A Opens the Library Record category.
Match Factor N/A The match factor with the hit spectrum.
Number of relative Extrema N/A The number of extrema in the hit spectrum.
Retention Index N/A The retention index of the hit spectrum.
Retention Time N/A The retention time at which the spectrum was extracted.
Sequence Header Record N/A Returns the selected information about the sequence from which the
spectrum was extracted. All variables in section 7.3 become available.
Sequence Name N/A The name of the sequence from which the spectrum was extracted.
Solvent Composition N/A Solvents used when measuring the hit spectrum.

Chromeleon 7

Spectrum Data N/A Provides details of the hit spectrum. Allows use of any variable from the UV
Spectrum category (see 7.17).
•Time offset only
7.19 Peak Tentative Identification
Amount Estimated amount of the peak.
CAS Number The CAS number of the tentatively identified component.
Int. Std. The internal standard peak used for calculating the estimated amount value.
Library Name Name of the MS library in which the hit spectrum was found.
Match Factor Match factor (SI) for the hit spectrum and the apex spectrum of the peak.
Name Tentative name of the peak.
Probability Probability that the hit spectrum and the apex spectrum of the peak are identical.
Reverse Match Factor Reverse Match Factor (RSI) for the hit spectrum and the apex spectrum of the peak.
7.20 Processing Method

Available algorithm version N/A Available version of the preferred algorithm type.
Detection Algorithm Select the algorithm to be reported.
Blank Run injection Record N/A Selected information about the injection that is specified as
fixed blank injection for chromatogram subtraction. All
variables in section 0 become available.
Calibration Level Name N/A Name of the amount column. The name can be selected as
follows:
•Current injection (default)
•Calibration level number

Chromeleon 7

Calibration Mode N/A Returns a text identifying the calibration mode as defined in
the Global Calibration Settings of the processing method, for
example, Total or Bracketed.
Comment N/A Processing method comment.
Composite Scoring N/A All variables in section 7.21 become available
Creation Date and Time Format date/time as text The processing method creation date and time can have the
following formats:
•Time offset only
Time in universal coordinated time The time in coordinated universal time standard format.
Time using local time zone The conversion of date and time to your local time zone with
the following formats:
•Time offset only
Creation Operator Full Name Full user name of the user who created the Processing
method.
Job Title Job title of the user who created the Processing method.
User Name User id of the user who created the Processing method.
Curve Fitting N/A Displays the curve fitting model selected in the processing
method.
Data Vault N/A Name of the corresponding data Vault.
Dead Time N/A The method dead time.
Delay Time N/A The delay time of the (2nd, 3rd) detector.
Delay Time Detector N/A The (2nd, 3rd) detector device name.
Detection Algorithm N/A Displays the detection algorithm used.
Directory N/A Directory where the processing method is saved.
Effective algorithm version N/A The version of the corresponding detection algorithm that is
stored in the processing method.
Is latest algorithm version N/A Reports whether the effective algorithm version is equal to the
currently available algorithm version in this Chromeleon
release.

Chromeleon 7

Last Fixed Calibration Update Date Format date/time as text The date and time of when the last update of the fixed
and Time calibration standards of a processing method was performed
can have the following formats:
•Time offset only
•Time offset only
Last Fixed Calibration Update Full Name Full user name of the user who last modified the fixed
Operator calibration standards of the Processing method.
Job Title Job title of the user who last modified the fixed calibration
standards of the Processing method.
User Name User id of the user who last modified the fixed calibration
standards of the Processing method.
Last Update Date and Time Format date/time as text The date and time of when the last update of a processing
method was performed can have the following formats:
•Time offset only
•Time offset only

Chromeleon 7

Last Update Operator Full Name Full user name of the user who last modified the Processing
method.
Job Title Job title of the user who last modified the Processing method.
User Name User id of the user who last modified the Processing method.
Matrix Correction Enabled N/A Displays if matrix correction is enabled or not.
MS Detection Algorithm N/A The name of the detection algorithm used for mass
spectrometry.
MS Library Screening Parameters N/A Returns the selected information about the library screening
parameters for mass spectrometry. All variables in section
7.22 become available.
MS Settings N/A Returns the selected information about the settings for mass
spectrometry. All variables in section 7.23 become available.
Name N/A Processing method name.
Number of Calibration Levels N/A Number of calibration levels in the Processing method.
Number of Components N/A The number of components in the component table.
Number of Detection Parameters N/A The number of detection parameters used.
Number of Test Cases N/A The number of the single test cases.
Number of Peak Groups N/A The number of peak groups.
Origin of Fixed Calibration N/A Original location of calibration standards in Fixed mode.
Standards
Parent Sequence Header Record N/A Returns the selected information about the sequence in which
the processing method is currently used. All variables in
section 7.3 become available.
Parent Sequence Name N/A The name of the sequence in which the processing method is
stored.
Reference Inject Volume N/A Reference injection volume setting for amount interpretation.
Retention Time Determination N/A Displays Retention Time Determination selected in the
processing method.
Select Component in the Select component in component Details about the components in the component table.
Component Table table Components can be selected as follows:
•by Name
•by Number
•by Group
•ISTD (Internal Standard)
•Reference Component
N/A All variables in section 7.28 become available.
Select Test Case Test Case Selection Returns the results of a system suitability test case. The test
case is selected using the following options:
Select by number
Select by name
Select Peak Group Select Peak Group Returns a specific peak group. The peak group record is
selected using the following options:
• by Name – the name of the peak group
• by Number – the number of the peak group if sorted by
the retention time
• by Group – the Peak Group(s) property of the peak
group record (see 5.3.4 for details)
Separate Calibration N/A Displays if dual column separate calibration mode is activated.

Chromeleon 7

Spectra Library Screening N/A Displays spectra library screening settings.
Parameters
Subtraction Mode N/A Displays the type of blank run subtraction used.
UV Spectra Settings N/A Displays the settings for UV spectra comparison and baseline
correction. All variables in section 7.26 become available.
Date & Time Date and time when the version was created. The same sub
functions as for other date & time variables are available
•Time offset only
Operator Information about the user who created the version. The
same sub functions as for other operator variables are
available. These are
7.21 Composite Scoring (Processing Method)
Amount Ratio Confirmation Channel Returns the confirmation channel used for amount ratio confirmation scoring as defined in
Amount Ratio Reference Channel Returns the reference channel used for amount ratio confirmation scoring as defined in the
processing method.
Amount Ratio Tolerance % Returns the pass/fail tolerance percentage (%) used for amount ratio confirmation as
defined in the processing method.
Fail Threshold Returns the overall composite scoring failure threshold.
Is Amount Ratio Used Returns whether or not amount ratio confirmation scoring is used.
Is Confirming Ion Ratio Used Returns whether or not confirmation ion ratios and ion coelution is used for scoring.
Is Isotopic Dot Product Used Returns whether or not isotopic dot product is used for scoring.
Is Mass Accuracy Used Returns whether or not mass accuracy is used for scoring.
Is Peak Apex Alignment Used Returns whether or not peak apex alignment is used for scoring.
Isotopic Dot Product Threshold Returns the pass/fail threshold for isotopic dot product scoring.
Mass Accuracy Threshold Returns the numerical value for mass accuracy scoring.
Mass Accuracy Unit Returns the mass accuracy threshold unit (PPM, MMU, or AMU) for mass accuracy scoring.
Pass Threshold Returns the overall composite scoring pass threshold.
Peak Apex Alignment Threshold Returns the pass/fail threshold for peak apex alignment scoring.

Chromeleon 7
7.22 MS Library Screening
Is MS Library Used Returns whether a selected library is searched during MS library screening. The MS
library is selected using the following options:
Select by number
Select by name
Match Threshold The threshold value set for Match Factor (SI).
Mol. Weight The molecular weight entered in the Search with Mol. Weight box.
MS Library The name of the selected MS library available for library screening. The MS library is
selected using the following options:
Select by number
Number of MS Libraries The number of MS libraries in the MS libraries to be searched.
Probability Threshold The threshold value (in %) set for Probability
Reverse Match Threshold The threshold value set for Reverse Match Factor (RSI).
Reverse Search Reports whether or not Reverse Search is selected.
Search Type The MS Library search type.
Search with Mol. Weight Reports whether or not Search with Mol. Weight is selected.
7.23 MS Settings
Baseline Correction The selected baseline correction method
Fixed Noise Reduction Threshold Reports a specified number of mass peaks with the greatest intensities included in the
spectrum.
Inhibit Integration for TIC Allows disabling integration for TIC. Especially useful for timed SIM and timed SRM
experiments.
Left Region Bunch The number of single spectra which are bunched (averaged) before the start of a
peak.
Manually Defined Mass Tolerance Reports whether a default mass tolerance has been manually defined.
Mass Tolerance The specified mass tolerance value which defines how many mass units before and
after a specified mass are included in an extracted ion chromatogram (XIC).
Mass Tolerance Unit The specified unit of a manually defined mass tolerance.
Maximum of Fixed Baseline Correction Range The maximum value of the specified retention time range. The range is selected using
the following options:
1st fixed range
2nd fixed range
Minimum of Fixed Baseline Correction Range The minimum value of the specified retention time range. The range is selected using
the following options:
1st fixed range
2nd fixed range
Noise Reduction Mode The defined mode to reduce noise.
Number of Smoothing Points The defined number of input data points used to generate each output data point.
Peak Spectrum Bunch The number of single spectra to be bunched (averaged) to form the spectrum at the
peak maximum.
Relative Noise Reduction Threshold The specified threshold value used to include only mass peaks with greater relative
intensities in the spectrum.
Right Region Bunch The number of single spectra which are bunched (averaged) after the end of a peak.
Smoothing Type The selected smoothing algorithm type applied to the data to reduce signal noise.

Chromeleon 7
7.24 System Suitability Test Case Details

Channel N/A Allows the selection of the channels on which the tests will be
performed
Evaluation Formula N/A Returns the evaluation formula used for the system suitability
test case.
Fail Actions N/A List of actions taken in if system suitability test fails.
Incomputable Interpretation N/A Displays the result of the system suitability test when the test
condition cannot be evaluated.
Injection Condition N/A Displays condition used to select the injections for the system
suitability test.
MaximumNumberOfInjections N/A Maximum number of injections for which a statistical
calculation is performed.
MinimumNumberOfInjections N/A Minimum number of injections for which a statistical
calculation is performed.
Name N/A Name of the system suitability test case.
Number N/A Number of the system suitability test case.
Number of Decimal Places N/A Specified decimal places to which the evaluation result and
reference value are rounded.
Number of Fail Actions N/A Number of fail actions for the test case.
Number of Pass Actions N/A Number of pass actions for the test case.
Operator N/A Comparison operator used to compare the values of the
evaluation formula with the specified reference value.
Pass Actions N/A Overview of actions that are executed.
Peak Specification N/A Condition used to select the peak for the system suitability test
case.
Reference Value Formula Return formula of Formula that is used to compare the ‘first’ or ‘second’
reference values to the evaluation formula.
Statistics N/A Result of the used statistics function.
7.25 Spectral Library Screening Parameters
Hit Threshold Hit threshold specified in the processing method.
Is Spectral Library Filter Active Returns if the spectral library filter is currently active.
Is Spectral Library Used Returns if a spectral library identified by number or name is used.
Library Spectral Filter Optionally selects that only spectra matching the defined conditions will be included in
the search
Match Criterion Match criterion specified for spectral library screening in the processing method (Least
Square, Weighted Least Square, or Correlation).
Number of Spectral Libraries Number of spectral libraries listed in the processing method.
Spectral Library Returns the name of a spectral library identified by name.
Spectrum Derivative Returns the spectrum derivative setting for spectral library screening defined by the
processing method.
Wavelength Range Maximum Maximum of the wavelength range used for spectral library screening.
Wavelength Range Minimum Minimum of the wavelength range used for spectral library screening.
7.26 UV Spectra Settings

Chromeleon 7
Baseline Correction Baseline correction mode for UV spectra specified in the processing method.
Left Region Bunch Left bunch width for peak-dependent baseline correction of UV spectra as specified in
Match Criterion Match criterion for UV spectra comparison specified in the processing method (Least
Square, Weighted Least Square, or Correlation).
Maximum of Fixed Baseline Correction Range Returns the end time of the (first or second) fixed baseline correction range for UV
spectra as defined in the processing method.
Minimum of Fixed Baseline Correction Range Returns the start time of the (first or second) fixed baseline correction range for UV
spectra as defined in the processing method.
Peak Purity Threshold Peak purity threshold value for UV spectra comparison defined in the processing
method.
Peak Spectrum Bunch Peak spectrum bunch width for UV spectra defined in the processing method.
Right Region Bunch Right bunch width for peak-dependent baseline correction of UV spectra as specified
in the processing method.
Spectrum Derivative Spectrum derivative setting for UV spectra comparison defined in the processing
method (None, 1st Derivative, or 2nd Derivative).
Wavelength Range Maximum End wavelength of the wavelength range that was used for UV spectra comparison.
Wavelength Range Minimum Start wavelength of the wavelength range that was used for UV spectra comparison.
7.27 Detection Parameters

The variables that Chromeleon can show are the same as the values that are defined in the processing method (see 5.3.1
for more details).
7.28 Component
The variables that Chromeleon can show are the same as the values that are defined in the component table in the
processing method (see 5.3.2 for more details).
7.29 Peak Group

The variables that Chromeleon can show are the same as the values that are defined in the peak group table in the
processing method (see 5.3.4 for more details).
7.30 Instrument Method
Comment Instrument method comment.
Creation Date & Time Format date/time as text The instrument method creation date and time can have the following
formats:
•Time offset only
time
your local computer (including any daylight savings time adjustments
that apply)

Chromeleon 7
following formats:
•Time offset only
Creation Operator Full Name Full user name of the user who created the instrument method.
Job Title Job title of the user who created the instrument method.
User Name User id of the user who created the instrument method.
Data Vault The data vault where the instrument method is stored.
Directory Directory where the instrument method is stored.
Instrument Name of the instrument associated with the instrument method.
Last Update Date & Time Format date/time as text The date and time of when the last update of an instrument method was
performed can have the following formats:
•Time offset only
time
that apply)
following formats:
•Time offset only
Last Update Operator Full Name Full name of the user who last saved changes to the instrument
method.
Job Title Job title of the user who last saved changes to the instrument method.
User Name User id of the user who last saved changes to the instrument method.
Name Instrument method name.
Server Name of the PC that the instrument was connected to.

Chromeleon 7
Date & Time Date and time when the version was created. The same sub functions
as for other date & time variables are available
•Time offset only
7.31 Mass Spectrometry
Device Information All variables in section 7.32 become available.
Mass Spectrum All variables in section 7.16 become available.
Spectra Count Number of mass spectra scans comprising the selected chromatographic peak.
Status Log Individual instrument status values recorded during the data acquisition.
Tune Data Values of individual tune data parameters.
7.32 MS Device
Device Name Name of device.
Firmware Version Device firmware version.
Hardware Version Device hardware version.
Model Model of device.
Name Name of device.
7.33 MS Detection Parameters

When Cobra or Chromeleon 6 algorithm is active, the variables that Chromeleon can show are the same as the values that
are defined in the processing method (see 5.3.1 for more details).
Algorithm Name of the detection algorithm (Cobra, Chromeleon 6, Genesis or ICIS) used for
mass spectrometry.
Area Noise Factor (ICIS) Noise level multiplier used to determine the peak edge after the location of the
possible peak.
Area Scan Window (ICIS) Number of scans on each side of the peak apex.
Area Tail Extension (ICIS) Number of scans past the peak endpoint used in averaging the intensity.

Chromeleon 7
Baseline Window (ICIS) Number of scans over which to look for a local minima.
Calculate Noise As (Genesis) Returns the specified parameter to calculate the signal-to-noise values as RMS or
Peak to Peak.
Constrain Peak Width (Genesis, ICIS) Constrained peak width of a component during peak integration of a chromatogram
Enable Valley Detection (Genesis) Enables / disables valley detection.
Expected Peak Width (Genesis) Expected peak width in seconds, provided that valley detection is enabled.
Minimum Peak Width Minimum number of scans in a peak.
Multiplet Resolution Minimum separation in scans between the apexes of two potential peaks.
Minimum Scans in Baseline (Genesis) Minimum number of scans specified to calculate a baseline.
Mulitplet Resolution (ICIS) Minimum separation in scans between the apexes of two potential peaks.
Noise Method (ICIS) Algorithm used for determining the noise level.
Peak Height (Genesis, ICIS) Percent of the total peak height (100%) that a signal is above the baseline before
integration is turned on or off.
Peak Noise Factor (ICIS) Noise level multiplier used to determine the potential peak signal threshold.
Peak S/N Cutoff (Genesis) Returns the specified peak signal-to-noise cutoff value.
Rise Percentage (Genesis) The defined percentage of the valley bottom that the peak trace can rise above a
baseline (before or after the peak) before valley detection peak integration criteria are
applied.
RMS (ICIS) The calculated noise as RMS.
S/N Threshold (Genesis) The current signal-to-noise threshold for peak integration.
Tailing Factor (Genesis, ICIS) Maximum ratio of the trailing edge to the leading side of a constrained peak.
Valley Depth (Genesis) Returns the signal-to-noise range used for valley detection.
7.34 Peptide
The Peptide category contains variables which were defined by a Pinpoint workbook import.
Charge Charge state of the peptide.
Chemical Formula Chemical formula of the component entered in the component table.
Composite Score Result of the composite scoring test.
Isotope Isotope related report variables. See section 7.35.
Isotopic Dot Product Isotopic dot product value used to evaluate isotopic dot product scoring.
Mass Accuracy Mass accuracy value used to evaluate mass accuracy scoring for the nth mass trace in the
mass trace settings list.
Molecular Mass Molecular mass of the component entered in the component table.
Name Peptide name.
Number of Charge States (Peptide Variable) Number of charge states of the peptide.
Number of Isotopes in Observed Isotopic Number of isotopes in the observed isotopic distribution.
Distribution
Number of Isotopes in Theoretical Isotopic Number of isotopes in the theoretical isotopic distribution.
Distribution
Observed Isotopic Distribution Observed isotopic distribution.
Peak Apex Alignment Standard deviation between confirming peak apexes.
Retention Time Nominal retention time defined in the component table.
Theoretical Isotopic Distribution Theoretical isotopic distribution.
Window/(Component) Identification Window settings defined in the component table.

Chromeleon 7
7.35 Isotope
The Isotope category is accessed by using the Isotope(n) variable of the Peptide category where n refers to the isotope
number.
Auto Filter Text definition of the scan filter that was used to select a mass spectrum at a specific
retention time.
Collision Energy Activation energy of the first precursor of the MS confirming peak, if a precursor is defined
by the filter.
End Time Ending retention time of the MS extraction
Extraction Time MS extraction time value, i.e. the retention time at which the apex of the peak is expected.
Extraction Window Settings Period of time which is subtracted from and added after the apex time at which the peak is
expected to create the retention time range.
Ion Coelution Ion coelution value of the peak ratio.
Mass Ranges List of the mass ranges used for the extraction of ion chromatograms.
Number of Smoothing Points Data points used for the selected smoothing algorithm to reduce noise.
Precursor Mass Mass of the first precursor of the MS confirming peak, if a precursor is defined by the filter.
Ratio Window Specified window width value (%) of the peak ratio assigned to the component.
Ratio Window Type Selected window type of the peak ratio assigned to the component: Absolute or Relative.
Smoothing Algorithm Name of the smoothing algorithm used to reduce noise.
Start Time Start retention time of the MS extraction.
Target Ratio Value of the peak target ratio assigned to the component.
7.36 Non-Targeted MS Processing

Non-Targeted MS Processing category variables may only be used in the Summary Table of the Report Designer category
or Interactive Results in the Data Processing category.
Algorithm Algorithm used for non-targeted MS processing
Alignment Bypass Whether the alignment step is bypassed or not
Alignment Min Intensity Minimum signal intensity for alignment algorithm to take into consideration
Correlation Bin Width Width, in Daltons, of MS segment to correlate reference TIC to unknown TIC data point
Description Text description of non-targeted MS processing experiment. Does not affect results
Frame Selects and creates the Frame category (see section 7.37) based on frame ID
m/z Max The start of the m/z range in which the algorithm is permitted to create a frame.
m/z Min The end of the m/z range in which the algorithm is permitted to create a frame
m/z Width The width (in ppm) of the frame created for signal detection
Max Threads Maximum number of logical CPU cores which the algorithm is allowed to run on
Maximum Frames Maximum number of frames that the algorithm is allowed to detect before stopping.
Name Name of the non-targeted MS processing experiment. Does not affect results
Peak Intensity Threshold Minimum signal intensity required to be observed for algorithm to define a frame as valid
Reference Index Injection number of reference when reference mode is set to Relative
Reference Mode Mode in which reference injection is defined – ‘Relative’ if based on an injection number,
‘Fixed’ if based on explicit injection inside or outside of sequence
Reference URI Path to reference injection if reference mode is set to Fixed.
Result Status Result of non-targeted peak detection after
RT Alignment Limits Maximum allowed retention time transformation of unknown TIC datapoint when aligning to
reference TIC

Chromeleon 7
Scan Filters MS scan filters used for non-targeted MS processing
Tile Increment Number of scans by which the tile size is incremented
Tile Maximum Maximum tile size
Tile Size Initial size (in number of scans) of a tile that correlates base peak alignment across the
reference and unknown injections
Tile Threshold Correlation threshold at which the tile size is incremented to the next larger size.
Time Start Start time of the range in which the algorithm is permitted to create a frame
Time Stop End time of the range in which the algorithm is permitted to create a frame
Time Width The width (in min) of the frame created for signal detection
Type Type of differential analysis carried out. Chromeleon only executes AvsB type experiments.
Version Version of algorithm used for non-targeted MS processing
7.37 Intact Protein Deconvolution

Intact Protein Deconvolution category variables may be used as standalone parameters or in the Summary Table of the
Report Designer category or Interactive Results in the Data Processing category.
Variable Sub-Variable Description

Chromatogram Chromatogram Type Type of plot displayed in the chromatogram pane.
Parameters
End Scan Number End scan number of the chromatographic data from which the source mass spectrum
will be extracted.
End Time Ending time of the chromatographic data from which the source mass spectrum will
be extracted.
Is High Sensitivity Whether the chromatographic peak detector performs a second pass at a higher
sensitivity.
Mass Range High Highest m/z value of the mass range used as input to the deconvolution.
Mass Range Low Lowest m/z value of the mass range used as input to the deconvolution.
Range Display Type Criterion used to determine the range of chromatographic data from which the source
mass spectrum will be extracted.
Relative Intensity Threshold Intensity threshold for peaks in the chromatogram.
Restricted Time Whether the entire chromatogram is displayed in the chromatogram pane.
Start Scan Number Beginning scan number of the chromatographic data from which the source mass
spectrum will be extracted.
Start Time Beginning time of the chromatographic data from which the source mass spectrum
will be extracted.
Multiconsensus Merge Tolerance Mass tolerance that components from individual files must satisfy to be merged into a
Merge Multiconsensus component.
Parameters
Merge Tolerance Type Unit of measure for the Merge Tolerance report variable.
Minimum Required Occurrences Minimum number of single raw data files that must be included in a Multiconsensus
component for it to be considered valid.
RT Tolerance Maximum separation in retention time that components from individual result files
must satisfy to be merged into a Multiconsensus component.
ReSpect Adduct Mass Custom adduct mass of a component.
Parameters
Charge Center Number of adduct ions used during electrospray (ESI) processing.
Charge High Maximum charge state to be deconvolved.
Charge Low Minimum charge state to be deconvolved.
Choice of Peak Model Index Appropriate peak model for the data.
Do Use Isotopic Profiles Whether isotopic profiles are used to identify components.

Chromeleon 7

High Number Adjacent Charges Maximum number of charge state peaks that must appear in a row for components of
the minimum output mass and maximum output mass.
Intensity Threshold Scale Intensity threshold scale required to display peaks in a chromatogram.
Is Calculate XIC Whether an extracted ion chromatogram (XIC) is calculated for each detected
component from a range of deconvoluted spectra.
Is PPM Tolerance Unit of measure for the mass difference of the same ion in different scans.
Low Number Adjacent Charges Minimum number of charge state peaks that must appear in a row for components of
the minimum and maximum output masses.
Mass Tolerance Global allowable error for the m/z values of peaks in a charge state series as they
appear in the input spectrum.
Min Peak Significance Numerical value (in standard deviations) that determines whether a peak is
considered legitimate and retained.
Negative Charge Whether the data was acquired in negative charge mode during the electrospray
(ESI) process
Noise Compensation Whether the ReSpect algorithm improves signal detection where the noise level
varies across the data.
Noise Rejection Degree of confidence that a peak is plausible.
Number of Peak Models Number of peak models generated to determine the width that a peak must have to
be associated with a compound.
Output Mass High Maximum value of the required mass range.
Output Mass Limit High Ending value of the output mass range.
Output Mass Limit Low Starting value of the output mass range.
Output Mass Low Minimum value of the required mass range.
Peak Model Width Scale Number of regions used to determine the peak width required for a peak to be
associated with a compound
Quality Score Threshold Minimum protein quality score required for a component to be considered valid.
Relative Abundance Threshold Height of the smaller overlapping isotopic cluster used to resolve overlapping isotopic
clusters.
Resolution at 400 m/z Resolution of the source spectrum at an m/z value of 400.
Target Peak Mass Expected target mass to use when calculating the peak model.
Target Peak Shape Left Numerical value for the left side of the peak (determines the peak sharpness required
for a peak to be associated with a compound).
Target Peak Shape Right Numerical value for the right side of the peak (determines the peak sharpness
required for a peak to be associated with a compound).
Result Apex RT
CV (coefficient of variation) percentage of the apex retention time of a component.
Component
Apex RT %CV Apex retention time of a component.
Charge State Count Number of charge states of a component.
Component ID Numerical position of a component in the component list.
Condition Condition of a component.
Delta Mass Delta mass of a component.
Detected Interval Count Number of detected intervals of a component in the injection results.
Drug Load Drug load of a component.
End Retention Time End retention time of the range of the chromatogram that you want to view.
Fractional Abundance Fractional abundance of a component.
High Charge State Range Maximum charge state to be deconvolved.
High Retention Time Maximum retention time of the range of the chromatogram that you want to view.
High Scan Range End scan of the range of the chromatogram that you want to view.
Intensity Sum of the intensities of the peaks for a charge state.

Chromeleon 7

Intensity Percent CV CV (coefficient of variation) percentage of the intensity of a component.
Low Charge State Range Minimum charge state to be deconvolved.
Low Retention Time Minimum retention time of the range of the chromatogram that you want to view.
Low Scan Range Beginning scan of the range of the chromatogram that you want to view.
Mass Mass of an identified component.
Mass Percent CV CV (coefficient of variation) percentage of the mass of a component.
Standard deviation of delta masses for all the charge states of an identified
Mass Std. Dev.
component, in Daltons.
Results obtained when matching the measured masses of components detected by
Matched Charges Chromeleon to the masses of target sequences specified by the user. (Opens the
Matched Charges report category.)
Matched Mass Error Error associated with the best target sequence that matches this component.
Modification of the target sequence that best matches a specific component within a
Modification
given tolerance.
Number of Files Observed Number of raw data files in which the component was detected.
Standard deviation of delta masses for all the charge states of an identified
PPM Std. Dev.
component, in parts per million.
Protein Name Name of the target sequence that matches this component within a given tolerance.
Ratio of the abundance of a specific peak to the abundance of the peak with the
Relative Abundance
highest abundance.
Score Quality score of a deconvolved component.
Score Percent CV CV (coefficient of variation) percentage of the score of a component.
Start Retention Time Starting retention time of the range of the chromatogram that you want to view.
Theoretical Mass Theoretical mass of a component.
Result The number of components in the deconvolution results.
Component
Count
Sliding Window
Average Width RT Retention time (width) of a sliding window.
Parameters
Maximum allowed separation in retention time between two successive individual
Biggest Gap RT
members of a merged component.
Numerical value indicating how close in mass two components in successive sliding
Merge Tolerance
windows must be to qualify as a single component.
Merge Tolerance Type Unit of measure for the Merge Tolerance report variable.
Minimum number of sliding window intervals that a component must appear in to be
Min Cycles
considered valid.
Offset Percent Offset between successive sliding windows as a percentage value.
Offset Scans Offset between successive sliding windows as a number of scans.
Offset Type Mode used to specify the offset between successive sliding windows.
Start Time Beginning of the retention time range that a single deconvolution applies to.
Stop Time End of the retention time range that a single deconvolution applies to.
Xtract
Adduct Mass Custom adduct mass of a component.
Parameters
Charge Carrier Type Type of adduct ion used during electrospray (ESI) processing.
Charge Range High Maximum charge state to be deconvolved.

Charge Range Low Minimum charge state to be deconvolved.
Tolerance toward errors when the spectrum intensity is much higher than expected
Consider Overlaps
for the theoretical isotopic cluster.
Custom Distribution Table Type of isotope table used.

Chromeleon 7

Allowable margin of error when calculating the ratio of the most abundant isotope to
Expected Intensity Error
the next isotope higher in mass in the isotope series.
Quality of a match between a measured isotope pattern and an averaging distribution
Fit Factor
of the same mass.
Whether an extracted ion chromatogram (XIC) is calculated for each detected
Is Calculate XIC
component from a range of deconvoluted spectra.
Whether data was acquired in negative charge mode during the electrospray (ESI)
Is Negative Ion
process.
Min Intensity Minimum intensity threshold used to filter out possible background noise.
Minimum Charge States Minimum number of charge states required to produce a component.
Output Mass Limit High Ending value of the output mass range.
Output Mass Limit Low Starting value of the output mass range.
7.38 Frame
The Frame category is accessed by using the Frame(n) variable of the Non-Targeted MS category where n refers to the
Frame ID or from the Report Formula Editor of the Frame Table.
Avg_intensity The average intensity of the peaks in the selected frame of the sample injection
Base Component Component ID of the pattern recognition cluster root element. If the PR Element variable is
less or greater than 0, the base component will return 0
Charge The expected charge state based on rudimentary observed isotopic mass distribution. This
does not take into account isotopic ratios.
Component ID Unique ID number of a component cluster after pattern recognition clustering
Component Score Returns the component score.
Frame ID Unique ID of the frame independent of any pattern recognition clustering
Mass Observed m/z for frame
Molecular Weight Molecular weight of frame adjusted for m/z ratio, charge state, and adduct
PR Element ID of a frame within a component cluster
PR Root Frame ID of root element within a component cluster
PR Size Number of elements within a component cluster
Ratio Unknown to reference ratio of AUC of signal – not to be confused with AUC of a peak
Reference_avg_intensity The average intensity of the peaks in the selected frame of the reference injection
Retention Time Retention time of the frame
Weighted Mass Weighted mass of the specified frame
7.39 Report Template
Creation Date & Time Format date/time as text The report template creation date and time can have the following
formats:
•Time offset only

Chromeleon 7
time
that apply)
following formats:
•Time offset only
Creation Operator Full Name Full user name of the user who created the report template.
Job Title Job title of the user who created the report template.
User Name User id of the user who created the report template.
Current Sheet Name The current sheet name
Current Sheet Number The current sheet number
Data Vault Name of data vault where the report template is stored.
Directory Directory where the report template is stored.
Last Update Date & Time Format date/time as text The date and time of when the last update of a report template was
performed can have the following formats:
•Time offset only
time
that apply)
following formats:
•Time offset only
Last Update Operator Full Name Full name of the user who last saved changes to the report template.
Job Title Job title of the user who last saved changes to the report template.
User Name User id of the user who last saved changes to the report template.
Name Name of the report template.

Chromeleon 7
Number of Sheets Number of sheets of the report template.
Date & Time Date and time when the version was created. The same sub functions
as for other date & time variables are available
•Time offset only
7.40 eWorkflow
These variables are only available to the eWorkflow editor.
Description Description of the eWorkflow.
Instrument Used Name of the instrument used by the eWorkflow.
Name Name of the eWorkflow.
State eWorkflow state.
Type eWorkflow Type.

Chromeleon 7
8 Electronic Signatures
Chromeleon supports the use of electronic signatures. The following signature levels are available:
• Submit
• Review
• Approve
Electronic signatures can be enabled and disabled for each sequence separately (see section 4.3.2.3). Electronic signatures
are automatically enabled for new sequences created with the Sequence Wizard. If new sequences are created with the
eWorkflow Wizard, the eWorkflow defines whether electronic signatures are enabled or not (see section 3.4.1.2).
On applying a signature, the following details are automatically recorded:
• User Name
• Full Name
• User Job Title
• Date and Time Signature was executed
• Signature Comment
The Electronic Signature process includes the creation of an electronic report (see section 5.8). The procedures for applying
electronic signatures are as follows:
8.1 Submit Signature

In the Console:
Select sequence to be signed in Data category.
Click the Submit button on the Sequence Control Bar.
–OR–
If the sequence is new or incomplete, click the down arrow next to the Submit button on the Sequence Control Bar and click
Submit.
If the electronic report does not yet exist, the Chromatography Studio window opens. Create the electronic report, and then
submit the sequence and report in the Studio.
In the Chromatography Studio:
In the Electronic Report category, on the Home ribbon, in the Signature group, click Submit button.
Signature dialog:
When the Submit Signature dialog box opens, enter your User Name and Signature Password.
(Optional) In the Comment box, add any comments that might be helpful. These comments will be displayed in the Console
on the Signature tab page in the sequence Properties dialog box and on the Signature State page in the Studio.
Click OK.
The electronic report changes to an electronic signature. After a sequence has been electronically signed, the sequence
cannot be modified unless the signatures are first removed. This protects sequence reports that have been accepted as
correct by "freezing" the current state of the results. In addition, the icon for the next signature step (if defined) is enabled.
When the sequence is signed a unique checksum is created and saved inside the sequence. Changes cannot be made to
the sequence without undoing the signature.
8.2 Review Signature

In the Console:
Click the down arrow next to the Review button on the Sequence Control Bar and click Review.

Chromeleon 7
In the Electronic Report category, on the Home ribbon, in the Signature group, click Review button.
Signature dialog:
Click OK.
8.3 Approve Signature

In the Console:
Click the down arrow next to the Approve button on the Sequence Control Bar and click Approve.
In the Electronic Report category, on the Home ribbon, in the Signature group, click Approve button.
Signature dialog:
Click OK.
8.4 Remove Signature

In the Console:
Select sequence in Data category.
Click the down arrow next to the Signed button on the Sequence Control Bar and click Remove Submit.
In the Electronic Report category, on the Home ribbon, in the Signature group, click Remove button.
Signature dialog:
Optional) In the Comment box, add any comments that might be helpful. These comments will be displayed in the Console
Click OK.
8.5 Verify Report

After a report has been signed, it can be checked at any time later to verify that the data is still free of unauthorized
manipulations.
In the Chromatography Studio, click the Electronic Report category bar and open an electronic report.
On the Home ribbon, in the Signature group, click Verify. You can monitor the report data being verified in the progress
window. When the progress bar has reached 100%, the verification process is completed.
8.6 Report Signed results
In the Chromatography Studio, click the Electronic Report category bar and open an electronic report.
On the Home ribbon, in the Print & Export group, you can either print or export to pdf the signed electronic report.

Chromeleon 7
9 Chromeleon Services Manager

The Chromeleon Services Manager (Figure 54) provides details on the status of the Chromeleon services. It also provides
access to the Instrument Controller Service and the Chromeleon Instrument Configuration Manager.
Figure 54: Chromeleon Services Manager
9.1 Instrument Controller Service

The following options are available for the instrument controller service:
Start Starts the Chromeleon instrument controller.
Stop Stops the Chromeleon instrument controller.
Start service on system start Starts the Chromeleon instrument controller automatically at computer startup.
Configure instruments Launches the Instrument Configuration Manager (see section 10).
9.2 Other Chromeleon services

The icon and text indicate the status of the other Chromeleon services. If any of the local or remote services become
unavailable, ‘Show Details’ becomes active. In order to manage other Chromeleon services or perform administrative tasks
open the Administration Console (section 11).

Chromeleon 7
10 Instrument Configuration Manager

The instrument configuration manager is the Chromeleon program that is used to connect instruments to the instrument
server.
New instruments are created here, and individual instrument modules are assigned. For a list of supported instruments
please refer to the “List of Supported Instruments” document. Figure 55 shows a typical instrument configuration.
Figure 55: Instrument Configuration Manager
10.1 Properties
The following instrument controller properties can be set:

within the Data Vault. These roles may differ from the login role of the user.
10.1.2 Queue Settings

Automatically upload finished remote sequences Allows automatic upload of sequences to remote location when finished.
Enforce Save Electronic Report Enforces that, for all Sequences created on this instrument, the Save Electronic
Report (after acquiring) option is selected and cannot be changed by a user
Enforce Print report Enforces that, for all Sequences created on this instrument, the Print report (after
acquiring) option is selected and cannot be changed by a user
Enforce Export report Enforces that, for all Sequences created on this instrument, the Export report (after
acquiring) option is selected and cannot be changed by a user
Enforce Print/Export report Enforces when, for all Sequences created on this instrument, any report will be
generated. Options are:

Chromeleon 7
Note: Instead of using access control on the Chromeleon instrument controller, it is possible to define access control for
each instrument on the instrument controller.

Chromeleon 7
11 Administration Console
The Chromeleon Administration Console (Figure 56) is a central access point for administrative tasks. In the Chromeleon
Administration Console, you can:
• manage users in the User Manager
• manage licenses in the License Manager
• plan and organize tasks with the Scheduler
• define global policies
• configure the discovery service and monitor other Chromeleon services
• manage data vaults
• manage Organizational Units
Figure 56: Administration Console
11.1 License Manager

This program provides licenses for all PCs running Chromeleon. There are 2 main license types – Instrument Controller and
Client. The License Manager can be used to manage the licenses. In the Chromeleon License Manager, you can
• assign client licenses to users, client stations, or instrument controllers
• assign instrument licenses to instrument controllers
• update your license
• check how many licenses are currently in use and how many are available
11.1.1 Client Licenses

The following license options can be granted to Clients:
License Option Description

Data Client License for data reprocessing on a network PC without instrument control. The
license supports multitasking and reports from the following partial methods:
single- and multiple-point calibration with various fit models, integration, ratio test,
user programs, etc.

Chromeleon 7

Instrument Operation Enables accessing a local or remote Instrument Controller for operating the
Instruments connected to the Controller.
Compliance Tools This license supports additional compliance features:
•Data Audit Trails and Versioning
•User management
Electronic Signatures
Report Designer Pro This license extends the report and calculation features. In addition, it supports
calculations using formulas and the functions listed in sections 5.7.22 and charts
(section 5.7.7).
Virtual Column Basic This license enables virtual column for isocratic analysis.
Virtual Column Complete This license enables virtual column including gradients.
Standard Instrument Integration Dedicated license for Standard instrument integration (SII).
SDK Developer Enables execution of un certified in-process SDK applications
SDK Runtime Enables execution of certified signed in-process SDK applications
Non-targeted MS Data Processing This license enables access to the Non-targeted MS Data Processing category
of the Studio
Intact Protein Deconvolution This license enables access to the Intact Protein Deconvolution category of the
Studio
11.1.2 Instrument Controller Licenses

The following license options can be granted to Instrument Controllers:

Instrument Controller The Instrument Controller license (without additional features) allows control and
signal acquisition without spectra from 6 Class 1instruments, of which 4 can be
fully controlled Dionex instruments. The number of Channels is not limited.
Instrument Class 1 The number of Class 1 instruments (= uncontrolled or Thermo Scientific
instruments) that can be connected to the Instrument Controller (up to a
maximum of 6). All instrument controllers are provided with this license.
Instrument Class 2 The number of Class 2 instruments (= third-party GCs) that can be connected to
the Instrument Controller (up to a maximum of 6).
Instrument Class 3 The number of Class 3 instruments (=third-party LCs) that can be connected to
the Instrument Controller (up to a maximum of 2).
3D Data Acquisition Additional license to acquire digital 3D data from 3D-capable detectors.
SQ / QqQ GC-MS Data Acquisition Enables recording of GC, single quadrupole and triple quadrupole MS data
LC-MS Data Acquisition Enables recording of LC-MS data for currently supported instruments.
IC Control SE A special low-cost control license for operating a single low-cost ion
chromatograph.
Fraction Collection Enables the fraction collection support.
The “Installation Mode” can be enabled or disabled. If enabled, administrators do not need to configure fixed license
features for the available instrument controllers. The instrument controller license request will be automatically assigned
without user interaction.
11.1.3 License Overview

The License Overview provides details of how many Client and Instrument Controller licenses are currently in use and how
many are available.
11.2 Scheduler
The Chromeleon 7 Scheduler is a service that handles all remote data processing requests in Chromeleon.

Chromeleon 7
11.2.1 Scheduler (Chromeleon Domain)
11.2.1.1 Task List
Enabled The user can disable or enable tasks. Tasks are only carried out if enabled.
New tasks can be created by clicking ‘Create new task’ button. Listed tasks can be edited by double click.
11.2.1.2 Audit Trail
Show audit trail records from … to … The audit trail lists scheduler events from the defined time period.
11.2.1.3 Service Account

Local System N/A The Local System account is a predefined local account of
the operating system.
User Account Domain Domain of user account to be used by scheduler service.
User User name to be used by scheduler service.
Password This is used to set the logon password for defined user.
Retype Password Confirmation of logon password for user.
The service account settings can only be changed after stopping the scheduler service.
11.2.1.4 Service Log
Show audit trail records from … to … The service log lists scheduler service events from the defined time period.
11.2.1.5 About
Delete entries older than … month(s) Change retention period setting of Scheduler Audit Trail
11.2.1.6 Scheduler Task
11.2.1.6.1 General

Name N/A Name of the task.
Owner N/A Displays the name of the owner of the task.
Description N/A (Optional) Free text entry to provide a more detailed
description of the tasks.
Enabled N/A Activates the task.
Specify additional settings that affect If the task fails, restart every: Specifies the time interval at which the Scheduler retries to
the behavior of the task start a task.
Attempt restart up to ... Specifies the number of attempts allowed to start a task. To
allow an unlimited (infinite) number of attempts to start the
task, select or type –1 in the times box.
11.2.1.6.2 Schedule
This page configures how often a task is scheduled.

Created N/A Date and time task were created.
Perform this task N/A Options to execute task; Manually, Hourly, Daily, Weekly, or
Monthly.

Chromeleon 7

Time Settings None Specify whether the task is started immediately or at a
specified time.
Every X hour(s) Specify whether the task is executed every hour or every
number of hours.
At a specified time every day. At … Specify time of day that task will be executed once a day.
At a specified day of the week. … Specify when the task is executed once a week at a
at …. specified day and time.
At a specified day of the month. On Specify when the task is executed once a month at a
… at …. specified day and time.
Expire N/A Specify a date after which the task will end.
11.2.1.6.3 Items
This page determines a predefined query that generates a result list of the source sequences to be copied or moved.
None Option if you do not want to transfer a sequence
Chromeleon 7 Defines the location of an existing injection query. Path of the predefined injection
query can be typed into the All sequences returned by query box or [...] can be
clicked to navigate to the required query.
Chromeleon 6 Copies existing sequences from a Chromeleon 6 data source. Chromeleon 6 User
ID and Password if required are entered into the given input boxes. Test button
checks whether login succeeded.
Path of the Chromeleon 6 query file can be typed into the All sequences returned
by query box or [...] can be clicked to navigate to the required query.
11.2.1.6.4 Action
This page views and manages the actions performed with the current task.
New Creates a new action item. The following actions can be created: copying a
sequence, moving a sequence and running an external program.
Remove Removes a selected action item from the list.
Destination Defines settings for the destination folder (Copy and Move tasks only):
Data vault: Select the destination data vault.
Folder formula: Type a name or formula in the box to determine the name of the
destination folder or alternatively click {...} to browse. Free text can also be typed to
determine a folder name.
If sequence in the destination folder already exists: Specifies the behavior of the
scheduler if a sequence with the same name already exists in the destination folder.
Options; Do not copy and Overwrite.
Select external program to be executed Defines settings for external programs: Program/script, Add arguments (optional),
Wait until external program terminates, Wait up to ... seconds and Do not wait for
external program to terminate.
11.3 User Database

The user database manages all Chromeleon user security functions such as user id and passwords, privilege and access
levels and electronic signature settings.
11.3.1 Toolbar
The tool bar has four buttons; The save policies button is enabled, if the policies have changed. The report button creates a
printable HTML file for the currently selected OrgUnit. The Audit Trail shows the User Management Audit Trail. The help
button shows the online help for the currently selected policy.

Chromeleon 7
11.3.2 User Database Policies

All global security policies are defined in this part of the user database (for example minimum password length).
11.3.2.1 Client Inactivity
Lock any client station that waits for Select this option to automatically lock the Chromeleon client if there has been no
user input (for example, the mouse is not used, and no keys are pressed)
Minutes without receiving user input Set a specified time of inactivity before client automatically locks.
Close the Chromeleon Console and Studio on any Select this option to automatically close the Chromeleon client if there has been no
client that waits for user input (for example, the mouse is not used, and no keys are pressed)
Note that if there are unsaved changes then the client will not be closed.
Minutes without receiving user input Set a specified time of inactivity before client automatically locks.
11.3.2.2 Logon User Name

Logon User Name Blank Ensures that the user name field of the logon window is
always blank.
Most Recent User Inserts the user name of the most recent user in the user id
field of the logon window.
Windows User Name Inserts the Windows user id into the user name field of the
logon window.
Force Windows User Name Inserts the Windows user id into the user name field of the
logon window. This user id cannot be changed.
11.3.2.3 LDAP Logon
Delegate password verification to the operating When activated the Chromeleon logon password verifications are delegated to the
system operating system. In the Domain/Domain controller enter the domain(s) to which
these settings shall apply.
Domain Controller Specify the domain or domain controller.
Allow silent logon with current windows user name When activated the Chromeleon logon is performed automatically with the Windows
and password credentials.
Exclude users from LDAP authentication Users excluded from LDAP authentication. Excluded users will use a separate
Chromeleon logon and signature password.
11.3.2.4 Password Character Sets

Password Character Sets Enforce at least … of the following Set requirement for passwords to contain a defined number
character sets for new passwords of characters (ranging from 0 to 4) from categories;
Lower case letters (a…z)
Upper case letters (A…Z)
Number (0…9)
Other characters
11.3.2.5 Minimal Password Length
Minimum password length Defines the minimum number of characters a user may use for their login and
signature passwords.

Chromeleon 7
11.3.2.6 Password Attempts

Locking Account/Signature Lock user’s account or signature Allows locking the user’s account after the set number of
permission, if corresponding trials entering the wrong password.
password is not entered correctly
Send email notification when a user Enable Checking this box will generate an email notification if a user
account is locked account is locked.
Mail recipient(s) Defines the email addresses (or Chromeleon usernames) to
whom the notification should be sent
Send email notification when a user Enable Checking this box will generate an email notification if the
signature password is locked signature password of a user account is locked.
Mail recipient(s) Defines the email addresses (or Chromeleon usernames) to
whom the notification should be sent
11.3.2.7 Password History
Number of recent passwords, that cannot be used Determines the number of unique recent passwords a user must use before an old
again password can be reused. It can be set between 0 and 20; if set to 0, then enforce
password history is disabled.
11.3.2.8 Electronic Signature
Submitter and Reviewer must be different When activated the user who submits the signed sequence must be different from
the user who reviews it.
Submitter and Approver must be different When activated the user who submits the signed sequence must be different from
the user who approves it.
Reviewer and Approver must be different When activated the user who reviews the signed sequence must be different from
the user who approves it.
Removing a signature requires the signature When enabled undoing a signature requires the user to enter a password.
password
A sequence will be ready for LIMS transfer When a sequence transitions Electronic Signature state, Chromeleon will inform an
external application (e.g. Thermo Scientific SampleManager LIMS) that the
sequence’s results are ready for transfer. Options are:
Never
When an electronic report is saved
When the sequence is submitted
When the sequence is reviewed
When the sequence is approved
* Requires appropriate external application add-in to be available to Chromeleon
client. In the case of SampleManager, this requires 12.1 SP1 or later.
11.3.2.9 Signature Programs

Run external application on signature N/A An external application can be run for each signature action
event in Chromeleon (Submit, Review, Approve, Remove
Signature).
Program file A program file can be associated that will be executed by the
console, after all other actions of a signature action have
been successfully finished.
Parameter Parameters can also be defined that will be evaluated in the
context of the sequence. The parameters may contain report
variables associated with Sequence, General and Global
Functions categories. Section 7.X

Chromeleon 7
11.3.2.10 Administrator Password Recovery

If a user with administrator privileges cannot logon to the Chromeleon AdminConsole any more (e.g. forgotten password,
account is locked) there is a procedure so that users with Windows administrator credentials can still logon to the
AdminConsole. To get this done you have to be a user with Windows administrator privileges on the computer where the
Chromeleon User Management Service is installed and running. The AdminConsole needs to be started with Windows
administrator credentials on this computer. After entering the wrong password for the user account which couldn’t logon
anymore a <Password Recovery> button appears on the Logon Dialog. Pressing this button, you have to enter the
password for the Windows administrator user account once again and after that you are logged on to the AdminConsole
successfully. The Administrator Password Recovery policy controls whether this procedure is possible or not.
If Organizational Units are enabled (see 11.4.2 for details) this user database policy is only available for the so-called
<Global> OrgUnit.
Option Description
Enable Allows to apply the password recovery procedure.
Disable Prevent the usage of the password recovery procedure.
Disable permanently Prevents the usage of the password recovery procedure permanently. Once this
option is saved there is no way to enable it again.
11.3.2.11 User Account Restrictions

If Organizational Units (OrgUnits) are enabled (see 11.4.2 for details) then these user database policies are only available
for the <Global> OrgUnit. All other OrgUnits must follow these policies.
Allow delete user accounts Controls whether user accounts can be deleted at all.
Allow rename user accounts Controls whether user names can be changed. Changing the casing of user names
is always allowed.
Allow reuse user names Controls whether user names which are deleted or renamed can be reused again.
11.3.3 Chromeleon Users

An unlimited number of users each having an enforced unique ID can be created. However, there is a limitation relating to
the maximum network message size (WCF quota). The limit depends on the length of user names, job titles, password
history, etc. but approximately equates to 100000 users.
11.3.3.1 Toolbar
The tool bar has six buttons; The Create New User button opens a wizard that guides you through defining user properties
(section 11.3.4) of the new user account. The Delete User(s) button will remove one or more users that are selected in the
user list. The Retire User(s) button deactivates one or more selected users in the list and invalidates the passwords (except
for users with LDAP authentication). The Reactivate User(s) button reverts one or more selected users in the list from the
retire state. The report button creates a printable HTML file of the list of users, including all user settings and memberships.
The help button shows the online help for the relevant section relating to managing users.
11.3.3.2 User List

The user list is a grid control that supports grouping and filtering. This grid control is read-only.
The following features are supported:
• Copy of rows to the clipboard (as simple text).
• Double-click on a row opens the according object for editing. The selection in the tree jumps to the object, the
editor control opens at the right side.
• Data can be sorted by one or multiple columns.
• Data can be grouped by one or multiple columns.
• Data can be filtered by one or multiple columns.
• The columns can be dragged to new positions.
• The column layout is preserved (saved in the user profile).

Chromeleon 7
11.3.4 User Properties

All security settings specific to a user id are set in this area of the database e.g. login and signature passwords, password
expiry settings, etc. When creating a new user, an existing user’s properties as detailed in this section can be cloned with
the exception of their passwords.
11.3.4.1 Toolbar
The toolbar has three buttons. The Save User button saves any change of the user properties. The Report button creates a
printable HTML file of the complete user database and the currently selected OrgUnit. The Reset Password button opens a
dialog to reset the password of the currently selected user.
11.3.4.2 General
User Name User name for logon and signature purposes. Once assigned this cannot be
modified. It is not possible to create duplicate user ID’s.
Full Name Full printed user name is entered here
Job Title An optional user job title can be entered here
Organizational Unit Associate organizational unit that user belongs to
Email Address Defines an email address that can be used for notifications
11.3.4.3 Password
Set the logon password This is used to set the logon password for a new user and is also used to reset a
user’s password. Passwords can be automatically generated.
The password cannot be changed by the user Prevents the user from changing their current password.
The user must change logon password on next logon. Forces the user to change their logon password when the next logon to
Chromeleon.
The password must be periodically changed Forces the user to change their logon password x
Day(s)/Week(s)/Month(s)/Year(s) after they last changed their password.
Account Locked Locks the account.
11.3.4.4 Signature Password
Set the signature password This is used to set the signature password for a new user and is also used to reset
a user’s signature password. Passwords can be automatically generated.
The password cannot be changed by the user Prevents the user from changing their current password.
The user must change the password on next Forces the user to change their signature password when performing their next
signature. signature action.
The password must be periodically changed Forces the user to change their signature password x
Day(s)/Week(s)/Month(s)/Year(s) after they last changed their password.
Signature Locked Locks the signature and prevents it being used.
11.3.4.5 Access Groups

Shows the access groups that a user is assigned to. It is possible to assign/un-assign access groups to a user here.
11.3.4.6 Roles
Default logon role Allows a default role to be preselected for every logon of a user, even if the last
logon was with a different role.
Select the Roles where the user will be a member Shows the roles that a user is assigned to. It is possible to assign/un-assign roles
to a user here.

Chromeleon 7
11.3.4.7 Manage Users

Allows to enable or disable detailed user administration rights. This page is only available for users with full administrator
rights in the user database.
Allow all user management operations Allows to this user all user database administration rights.
Manage user database policies Controls whether this administrator user can change anything in the user database
policies
Manage access groups Controls whether this administrator user can create, delete or modify access
groups in the user database.
Manage roles Controls whether this administrator user can create, delete or modify roles in the
user database, e.g. to enable a certain privilege in a role.
Create users Controls whether this administrator user can create users using the ‘Create New
User’ wizard.
Create users via clone Controls whether this administrator user can create users via cloning an already
existing one even though the ‘Create users’ option is disabled.
Cloneable Users … Defines the users this administrator user can select when creating a new user via
the clone mode.
Modify users Controls whether this administrator user can change any property (e.g. Full user
name, Title, etc…) of any user record in the user database. Assigning new access
groups or roles is controlled via a further option.
Reset password of users Allows this administrator user to reset the password of any user in the user
database even though the ‘Modify users’ option is disabled.
Delete users Controls whether this administrator user can delete users. The Delete Users option
is only available if the corresponding user database policy option (User Account
Restrictions -> Allow delete user accounts) is enabled.
Assign access groups Controls whether this administrator user can assign access groups to any user
record.
Assignable access groups … Defines those access groups which can be used by this administrator user when
he wants to assign access groups to any user record.
Assign roles Controls whether this administrator user can assign roles to any user record.
Assignable roles … Defines those roles which can be used by this administrator user when he wants to
assign roles to any user record.
Copy settings from … Copies settings of the Manage User page from another user record.
11.3.4.8 Profiles
Name Functional area of Chromeleon (read-only) that has been stored to the user’s
profile.
Value Details of the change (read-only) that was made and stored to the user’s profile.
11.3.5 Access Groups

An unlimited number of access groups can be created, and an unlimited number of users can be placed in each access
group. These groups can be assigned to Chromeleon Data Vaults (4.1) and folders (4.2), and also the Chromeleon
Instrument Controller and Instruments (9). Once assigned, only members of the groups will be able to access the objects.
Access groups are given a unique name and can also be given a description. One access group can be assigned to one
organizational unit, but must be uniquely identified across all organizational units that exist in the Chromeleon Domain.
11.3.5.1 Toolbar
The tool bar has four buttons; The Create New Access Group button opens a dialog to define Access Group name and
description. The Delete Access Group(s) button will remove one or more access groups that are selected in the access
group list. The report button creates a printable HTML file of the list of access groups, including all access group settings
and members. The help button shows the online help for the relevant section relating to managing users.

Chromeleon 7
11.3.5.2 Access Group List

The access group list is a grid control that supports grouping and filtering. This grid control is read-only.
• Double-click on a row, opens the according object for editing. The selection in the tree jumps to the object, the
• The column layout is preserved (saved in the user profile
11.3.6 Roles
An unlimited number of roles can be created in Chromeleon and an unlimited number of users can be assigned to each role.
A user may be assigned to more than 1 role and each role can have different privilege settings (section 11.3.6.3).
One role can be assigned to one organizational unit, but must be uniquely identified across all organizational units that exist
in the Chromeleon Domain.
11.3.6.1 Toolbar
The tool bar has four buttons; The Create New Role button opens a dialog to define Role name, description and privileges.
The Delete Role(s) button will remove one or more roles that are selected in the roles list. The report button creates a
printable HTML file of the list of roles, including all role settings, privileges and members. The help button shows the online
help for the relevant section relating to managing users.
11.3.6.2 Roles List

The access group list is a grid control that supports grouping and filtering. This grid control is read-only.
• Double-click on a row, opens the according object for editing. The selection in the tree jumps to the object, the
• The column layout is preserved (saved in the user profile
11.3.6.3 General
The privileges that can be assigned to each role are as follows:
11.3.6.3.1 Instrument Configuration

• Modify Instrument Controller Security Settings • Modify Instrument Configuration
• Modify Instrument Security Settings
11.3.6.3.2 ePanel
• Create ePanel • Add ePanel
• Delete ePanel • Export ePanel
• Design ePanel • Import ePanel
11.3.6.3.3 Instrument Method

Chromeleon 7
• Create Instrument Method • Copy Instrument Method

• Delete Instrument Method • Move Instrument Method
• Modify Instrument Method • Rename Instrument Method
• Modify Instrument Method Script
11.3.6.3.4 Daily Instrument Audit Trails

• Copy Instrument Audit Trail • Delete Instrument Audit Trail
• Move Instrument Audit Trail • Rename Instrument Audit Trail
11.3.6.3.5 Instrument Control

• Control Instrument • Change Qualification Interval
• Take Over Instrument Control • Override Qualification
• Control Queue • Approve Qualification
• Control Instrument while Queue Is Running • Manual Injection
• Change Performance Limit • Execute On-demand MS Auto tune /Calibration
• Execute On-demand MS Manual Tune /Calibration • Execute On-demand MS Auto Tune /Calibration in
a Sequence
11.3.6.3.6 Data Vault Basics

• Create Data Vault • Modify Security Settings
• Mount/Dismount Data Vault • Modify List of Custom Variables
• Rename Data Vault • Restore Versions
• Modify Versioning Mode • Modify List of Custom Formulas
11.3.6.3.7 Folders
• Create Folder • Move Folder
• Delete Folder • Make Folder Read-Only
• Rename Folder • Remove Folder Read-Only
• Copy Folder • Modify Folder Security Settings
11.3.6.3.8 Queries
• Create Query • Move Query
• Delete Query • Execute Query
• Modify Query • Rename Query
• Copy Query
11.3.6.3.9 Sequences
• Create Sequence • Rename Sequence with Raw Data
• Create Sequence via Wizard • Copy Sequence
• Create Sequence via eWorkflow • Move Sequence
• Create Sequence via Save As • Delete Sequence
• Create Sequence via Save As with Raw Data • Delete Read-Only Sequence
• Create Sequence from Injection Query Results • Make Sequence Read-Only
• Create Sequence from Worklist • Remove Sequence Read-Only

Chromeleon 7
• Modify Sequence • Modify Running Sequence

• Rename Sequence • Rename Sequence
• Modify When Visible Views are Updated •
11.3.6.3.10Injections
• Copy Injection • Delete Finished or Interrupted Injection
• Add New Injection • Delete Individual Channel/Audit Trail
• Insert New Injection Between Finished or • Lock Injections
Interrupted Injections
• Modify Finished or Interrupted Injection • Unlock Injections
• Modify Status of Already Finished or Interrupted
Injection
11.3.6.3.11eWorkflow
• Create eWorkflow • Run eWorkflow ‘Ready’
• Modify eWorkflow • Run eWorkflow ‘Retired’
• Rename eWorkflow • Send eWorkflow to File
• Delete eWorkflow • Import eWorkflow from File
• Run eWorkflow ‘Approved’ • Override Access Control
• Run eWorkflow ‘In Development’ • Modify When Visible Views are Updated
11.3.6.3.12Manual Data Processing

• Manipulate Peaks • Delete Peak Manipulations
• Edit Injection Specific XIC Detection Settings •
11.3.6.3.13Processing Methods
• Create Processing Method • Move Processing Method
• Delete Processing Method • Rename Processing Method
• Modify Processing Method • Manage Component Variables
• Copy Processing Method • Update Detection Algorithm Version
11.3.6.3.14Spectral Libraries
• Create Spectral Library • Move Spectral Library
• Delete Spectral Library • Rename Spectral Library
• Modify Spectral Library • Add Spectrum
• Copy Spectral Library • Delete Spectrum
11.3.6.3.15Report Templates
• Create Report Template • Copy Report Template
• Delete Report Template • Move Report Template
• Modify Report Template • Protect Report Template
• Rename Report Template • Unprotect Report Template
11.3.6.3.16Electronic Report
• Create Electronic Report • Move Electronic Report

Chromeleon 7
• Delete Electronic Report • Print Electronic Report

• Copy Electronic Report • Export Electronic Report
11.3.6.3.17Reporting
• Print Results • Export ADF
• Export PDF • Print or Export Unsaved Data
• Export XLS • Call External Program
• Export Text • Modify Default Print Settings
• Export AnDI • Modify Default Export Settings
• Export GAML • Allow Formula Customization
• Export Raw File • Modify Custom Formulas
11.3.6.3.18View Settings
• Create View Settings • Rename View Settings
• Delete View Settings • Copy View Settings
• Modify View Settings • Move View Settings
11.3.6.3.19Electronic Signatures
• Sign as Submitter • Remove Signature when Reviewed
• Sign as Reviewer • Remove Signature when Approved
• Sign as Approver • Modify Signature Requirements
• Remove Signature when Submitted
11.3.6.3.20Archive
• Import Chromeleon Data • Send to File
• Import Non-Chromeleon Data
11.3.6.3.21Administration
• Manage User Database • Overwrite Default Comment
• Manage Licenses • Modify Global Security Settings
• Manage Global Policies • Close Locked Clients
• Manage Scheduler • Revoke Data Transaction Lock
• Manage eWorkflow Tags • Manage Maintenance Window
• Manage Privileged Actions • Manage Updater Service and Repository
11.3.6.3.22Chromeleon XPS
• Manage User Interface • Use Client User Interface
11.3.6.4 Logon
Logon Role Defines whether or not role members can select the role when logging on.
Use special set of access groups Enables a set of access groups to be defined for the role which replace the access
groups of the user at logon.

Chromeleon 7
11.3.6.5 Members
Role Members Defines the users that are members of the role.
11.3.6.6 Licenses
Select the licenses requested from license service, if Licenses that will be requested from the Chromeleon client when the role is
this role has been selected as logon role selected at logon.
11.3.7 Audit Trail

Chromeleon logs information about all events related to the user database in User Database Audit Trails.
Show audit trail records from recent … months from The audit trail lists the changes to the user database from the first day of the
… to … previous month to the current date. Change the number of previous months to be
displayed. Type or select the preferred time period.
Show logon events To display all successful and failed logon operations.
Report Creates a report containing the current records of the User Database Audit Trail.
11.4 Global Policies

Global policy settings that apply for all networked computers running Chromeleon connected to the same Chromeleon
domain.
11.4.1 Toolbar
The tool bar has four buttons; The Save Policies button is enabled, if the policies have changed. The Report button creates
a printable HTML file for the currently selected OrgUnit. The Audit Trail button creates a printable HTML file of the list of
roles, including all role settings, privileges and members. The help button shows the online help for the currently selected
policy.
11.4.2 User Mode

Enable User Mode Enables or disables user mode. With disabled user mode, the user database
cannot be modified.
Enable Organizational Units Enables or disables Organizational Units. In the navigation tree the User
Database node is replaced by an Organizational Units node.
11.4.3 Host Name Resolution

Host Name Resolution Use names provided by Chromeleon uses the network address provided by the
workstations (default) workstation
Always use NetBIOS names. If the check box is selected, then the client will convert any
Check this if your network does not fully qualified domain names (FQDNs) in resource addresses
fully support DNS. to simple NetBios names before attempting communication
with the resource. This solves a problem for users where the
network uses WINS resolution only (i.e. no DNS) for the
intranet and where TCP/IP settings for some workstations
within that intranet causes them to publish FQDNs to
discovery. Users whose Chromeleon domain spans multiple
Windows domains should not use this option.

Chromeleon 7

Always use Fully Qualified Domain If the check box is selected, then Chromeleon will convert
names. Check this if your network any NetBIOS names in resource addresses to fully qualified
only resolves FQDNs. domain names before attempting communication with the
resource. This solves communication problems caused by
networks that resolve only fully qualified domain names, not
short domain names.
11.4.4 Multi-User Logon

Allow multiple users to logon within the same windows If enabled, concurrent access to Chromeleon by multiple users on the same PC
session concurrently is allowed.
When a user logs on, lock all other client sessions If enabled, client sessions of all other users on the same PC are locked as soon
as another user logs on.
11.4.5 Injection Locking

Enable locking of single injections If enabled, locking and/or unlocking of injections in the Console or
Chromatography Studio is allowed.
11.4.6 Remote Data Vaults

Show local Data Vaults of remote systems You can either show all data vaults when the function is enabled or hide remote
local data vaults from the data tree to show only data vaults that are local on your
computer, network data vaults, and data vaults marked favorite.
11.4.7 Instrument Audit Trails

Automatically archive instrument audit trails If enabled, the scheduler will copy daily instrument audit trails to the location
configured in ‘to’ field.
Automatically delete instrument audit trails If enabled, the scheduler will delete daily instrument audit trails older than the
configured time range.
11.4.8 Detection Algorithm Version

Offer option for existing processing methods to update to Select the check box if it is desirable to allow users an upgrade option for existing
the latest detection algorithm version processing methods during use.
Detection Algorithm Version Select how to handle stored detection algorithm version with options to either
keep currently used or update to latest, in a processing method for each of the
specific creation actions:
Create sequence from worklist
Create sequence via “Save As…”
Create sequence via eWorkflow
Create sequence via wizard
11.4.9 User Templates Location

User Templates Locations User specified locations that can store user created reporting object templates
which can then be listed as categories. Locations can be specified for;
Report Templates
Report Tables
Plots
Result Charts

Chromeleon 7
11.4.10 Watermark
Print with watermark If enabled, reports printed by Chromeleon will have a watermark.
11.4.11 UI Customizations
Display “QC Sample” for injections of type “Check If enabled, all visual references to “Check Standards” in the Console, Studio and
Standard” Reports will be replaced with “QC Sample”. When a sequence is created, this
setting is saved with the sequence. Thereafter, when the sequence is viewed, if
the stored setting does not match the current system setting, a message is
displayed.
Show injection Target mass detection columns If enabled, the following columns will be available for display in the sequence
table:
Target Formula or Mass
Target Negative Adducts
Target Positive Adducts
Show Non-Targeted MS Processing category If enabled, Non-Targeted MS Processing category is available to be accessed in
the studio
Show Intact Protein Deconvolution category If enabled, Intact Protein Deconvolution category is available to be accessed in
the studio
11.4.12 Privileged Actions

Settings Requires Authorization Select authorization and/or comment requirements for users when they
perform a specific operation. Privileged actions apply to all Data Vaults
that have the Versioning and Privileged Actions enabled (see section
Requires Comment 4.1.2). Privileged actions authorization and/or comments settings can be
enabled or disabled using the Select All or None buttons or using the
grouping or individual check boxes.
Default Comment The Default Comment can be any free text or can be one entry selected
from the Standard Comments tab.
Standard Comments N/A To help users save time and to keep wording consistent in audit trails,
you can create a list of standard comments. All users select from the
same list.
11.4.13 Email Configuration

Test Configuration button tests the configured email notification settings and sends an email to the recipient(s) if successful.
Sender Enter the email address of the sender.
Mail Server Address Enter the mail server address.
Enable TLS/SSL connection Click this check box to use TSL/SSL when connecting to the mail server.
Port Number Enter the Port Number of the mail server you want to connect to.
Authenticate on SMTP Server using logged on User Select which credentials to use for sender authentication on the mail server. If
Credentials the check box is checked the credentials of the currently logged on user will be
used otherwise enter the email address and password of the Authentication
User.
11.4.14 Station Audit

Enable Station Audit Trail logging If enabled, Station Audit Trail logging will be active.
11.4.15 License

Chromeleon 7

Enable notifications Checkbox Enables the notifications
when license is about
to expire or when Mail recipient(s) Defines one or more email addresses (or Chromeleon
license is in grace usernames) to whom the notifications will be sent
period Notifications sent when the time to Defines (in days) the time before expiration that the
license expiration is less than notifications will begin to be sent.
Resend email notifications every Defines (in hours) how often the notifications will be sent.
11.4.16 Raw Data

Enable raw data verification If enabled, Chromeleon will validate raw files to verify data integrity.
11.5 Define Policies in Organizational Units

If Organizational Units are enabled, each organizational unit contains modules for User Database Policies and Global
Policies which can have inherited or independent policy settings.
11.5.1 Separate Policy Settings for Organizational Units

If Organizational Units are enabled the following option is available in the Global Policies and User Database Policies
modules of the <Global> Organizational Unit:
Allow separate policy settings for Organizational Units This policy is locked by the <Global> organizational unit. All changes
apply to all organizational units. Click the check box to unlock the
policy so it can be changed for other organizational units.
This policy can be changed for other organizational units. Changes to

the policy affect the <Global> organizational unit and all organizational
units which use the global settings for this policy. Deselect the check
box to lock the policy so it can only be changed in the <Global>
organizational unit.
11.5.2 Use <Global> Settings

This option is available in the Global Policies and User Database Policies modules of all other organizational units, but only
available if the ‘Allow separate policy settings for Organizational Units’ check box in the <Global> organizational unit is
enabled:
Use <Global> Settings The check box is checked by default. The policy uses the settings of
the <Global> organizational unit. Clear the check box to enable
different settings for the organizational unit.
The check box is cleared. Independent policy settings are enabled.

Select the check box to use the global settings.
11.6 eWorkflow Tags

Tags for eWorkflows can be defined which can then be used to organize and group eWorkflows to reduce a large list of
eWorkflows to those eWorkflows which are relevant for the respective user.
11.6.1 Toolbar
The tool bar has three buttons; The Create New Tag button used to generate predefined eWorkflow tags. The Delete Tag
button removes the selected eWorkflow tag from the predefined list in the Administration Console. The help button shows
the online help for eWorkflow tags in Administration Console.

Chromeleon 7
11.6.2 Create New Tag

Tag Name User defined name for Tag.
Comment Optional comment providing description of tag.
11.7 Domain Resources

The Domain Resources displays summary information from the Discovery service of all Chromeleon Consoles, computers,
Instruments, Instrument Controllers, Data Vault Services, and Data Vaults currently registered with the Chromeleon Domain
Controller. There are separate tree nodes for each supported service type (All Resources, Computers, Data Vaults,
Instruments, Chromeleon Consoles and System Printers) which when selected display a tab page with aggregated data
items. The grid control on each tab page supports grouping and filtering and is read-only. Information in these tables can
help you manage the domain and troubleshoot problems.
11.7.1 All Resources
11.7.1.1 Toolbar
The tool bar has ten buttons; The Save button saves changes after removing an item from the table. The report button
creates a printable HTML file of the list of resources. The Audit Trail button displays the Data Audit Trail window for domain
resources. The Manage Data Vaults displays the Data Vault Manager if the selected item is a local data vault service. The
Show Vault Properties displays the Data Vault Properties for a selected data vault. The Configure Instrument button opens
the Instrument Configuration Manager connected to instrument controller of the selected instrument with that instrument
expanded in the tree. The Configure Instrument Controller button opens the Instrument Configuration Manager connected to
the selected instrument controller. The Updater Repository button opens the Updater Repository window if the selected item
is an Updater (see 11.7.1.3). The Add System Printer opens the Add System Printer window if the selected item is a Print
Service (see 11.7.1.4). The Remove button removes the selected item(s) from the table view only.
11.7.1.2 All Resources Context Menu

Manage Data Vaults... Displays the Data Vault Manager if the selected item is a local data vault service. If the data vault
service is remote, an error message is displayed. If more than one data vault service is selected in
the grid control the option is greyed out.
Show Data Vault Properties... Displays the Data Vault Properties for the selected data vault. If more than one data vault is
selected in the grid control the option is greyed out.
Show Data Vault Manager Audit Displays the Data Audit Trail window for the selected Data Vault Manager.
Trail...
Configure Instrument... Displays the Instrument Configuration Manager connected to the selected instrument. If
configuration of the instrument PC is already active or not possible, an error message is displayed.
If more than one instrument is selected in the grid control the option is greyed out.
Configure Instrument Controller... Displays the Instrument Configuration Manager connected to the selected instrument controller. If
the Instrument Configuration Manager is already active or establishing a connection is not possible,
an error message is displayed. If more than one instrument controller is selected in the grid control
the option is greyed out.
Show Instrument Configuration Audit Displays the Data Audit Trail window for the selected instrument controller.
Trail...
Updater Repository Opens the Updater Repository window if the selected item is an Updater (see 11.7.1.3)
Show Station Audit Trail... Displays the Data Audit Trail window for the host computer of the selected item.
Add System Printer... Displays the Add System Printer window if the selected item is a Print Service (see 11.7.1.4)
Edit System Printer... Displays the Edit System Printer window if the selected item is a Printer (see 11.7.1.5)
Remove Removes the selected item(s) from the table view only.
11.7.1.3 Updater Repository window

Displays the contents of the Updater Repository on the target computer.
11.7.1.3.1 Toolbar

Chromeleon 7
The toolbar has three buttons; The Empty button empties the Updater Repository on the target computer. The Delete
button deletes the selected package from the Updater Repository on the target computer. The Refresh button refreshes the
view.
11.7.1.4 Add System Printer window
Available Printers on <target Print Allows a printer configured on the target Print Service computer to be selected for use as a System
Service computer> Printer
Alias Enter a name by which the System Printer will be known throughout Chromeleon
Org. Unit Displays the Organizational Unit to which the selected Print Service computer belongs
11.7.1.5 Edit System Printer window
Available Printers on <target Print Allows a printer configured on the target Print Service computer to be selected for use as a System
Service computer> Printer
Alias Displays the name by which the System Printer is known throughout Chromeleon
Org. Unit Displays the Organizational Unit to which the selected Printer’s Print Service computer belongs
11.7.2 Computers
11.7.2.1 Toolbar
The tool bar has eight buttons; The Save button saves changes after removing an item from the table. The report button
resources. The Create Updater Package button opens the Create Updater Package wizard (see 11.7.2.4). The Manage
Data Vaults displays the Data Vault Manager connected to the data vault service of the selected computer. The Configure
Instrument Controller button opens the Instrument Configuration Manager connected to the selected instrument controller.
The Set Maintenance Window opens the Maintenance Windows Settings for the selected computer(s) (see section
11.7.2.3). The Updater Repository button opens the Updater Repository window for the selected computer (see section
11.7.1.3).
11.7.2.2 Computers Context Menu

Manage Data Vaults... Displays the Data Vault Manager if the selected item is a local data vault service. If the data vault
service is remote, an error message is displayed. If more than one data vault service is selected in
the grid control the option is greyed out.
Show Data Vault Manager Audit Displays the Data Audit Trail window for the selected Data Vault Manager.
Trail...
Configure Instrument Controller... Displays the Instrument Configuration Manager connected to the selected instrument controller. If
the Instrument Configuration Manager is already active or establishing a connection is not possible,
an error message is displayed. If more than one instrument controller is selected in the grid control
the option is greyed out.
Trail...
Set Maintenance Window... Displays the Maintenance Windows Settings for the selected workstations (see section 11.7.2.3).
Updater Repository Displays the Updater Repository window for the selected computer (see section 11.7.1.3)
11.7.2.3 Maintenance Window Settings

The Maintenance Window Settings prevent the selected workstation(s) displayed in the Computers Summary from using
instruments configured in Chromeleon for a set time.

Chromeleon 7

Define Maintenance Window N/A Select to enable all other options. If the workstation is currently under
maintenance, clearing the check box cancels the maintenance window.
Start of maintenance Enter the start dates and times of the maintenance window.
period
End of maintenance Enter the end dates and times of the maintenance window.
period
Open Ended Select this check box to remove the End of maintenance period setting
and keep the maintenance window open-ended.
In time zone Select the time zone of the selected workstation. If the workstation's time
zone is different from your local time zone, your corresponding local start
and end times are displayed below the Start of maintenance period and
End of maintenance period.
Notification period Select how far in advance users are notified of the maintenance window.
Select from the predefined settings or by manually entering the days and
hours.
Enforce maintenance Allows the user to select when to start enforcement:
window •Don’t enforce stop
•Stop after completed sequence
•Stop after completed injection
Download software Allows the selection of a Chromeleon Updater Package for installation
update during the Maintenance Window
11.7.2.4 Create Updater Package wizard

The Create Updater Package wizard guides the user through the process of creating an Updater Package for installation
during a Maintenance Window. The following parameters are defined by the Wizard:
Package Source Defines the folder containing an installation package.
Package Name Defines the name by which the package will be known throughout Chromeleon..
11.7.3 Data Vaults
11.7.3.1 Toolbar
The tool bar has six buttons; The Save button saves changes after removing an item from the table. The report button
resources. The Manage Data Vaults displays the Data Vault Manager connected to the data vault service of the selected
computer. The Show Vault Properties displays the Data Vault Properties for a selected data vault. The Remove button
removes the selected item(s) from the table view only.
11.7.3.2 Data Vaults Context Menu

Manage Data Vaults... Displays the Data Vault Manager and connects to the data vault service of the selected computer.
If the data vault service is remote, an error message is displayed. If more than one data vault is
Show Data Vault Properties... Displays the Data Vault Properties for the selected data vault. If more than one data vault is
Show Data Vault Manager Audit Displays the Data Audit Trail window for the Data Vault Service of the selected Data Vault.
Trail...
Remove Removes the selected item from the table view only.

Chromeleon 7
11.7.4 Instruments
11.7.4.1 Toolbar
The tool bar has five buttons; The Save button saves changes after removing an item from the table. The report button
resources. The Configure Instrument button opens the Instrument Configuration Manager connected to instrument controller
of the selected instrument with that instrument expanded in the tree. The Remove button removes the selected item(s) from
the table view only.
11.7.4.2 Instruments Context Menu

Configure Instrument... Displays the Instrument Configuration Manager connected to the selected instrument. If
configuration of the instrument PC is already active or not possible, an error message is displayed.
If more than one instrument is selected in the grid control the option is greyed out.
Trail...
11.7.5 Chromeleon Consoles
11.7.5.1 Toolbar
The tool bar has four buttons; The Save button saves changes after removing an item from the table. The report button
resources. The Remove button removes the selected item(s) from the table view only.
11.7.5.2 Chromeleon Consoles Context Menu

11.7.6 System Printers
11.7.6.1 Toolbar
The tool bar has four buttons; The Save button saves changes after removing an item from the table. The report button
resources. The Remove button removes the selected item(s) from the table view only.
11.7.6.2 System Printers Context Menu

Edit System Printer... Displays the Edit System Printer window for the selected item (see 11.7.1.5)
11.8 Local Machine

This page provides tools to manage resources on the local machine, i.e. the computer the administration console is running
on.

Chromeleon 7
11.8.1 Manage Data Vaults
11.8.1.1 Data Vault Manager

The Data Vault Manager (Figure 57) enables a user to create, upgrade, mount, or dismount and configure Chromeleon Data
Vaults.
Figure 57: Data Vault Manager


Local Data Vaults Lists all Chromeleon 6 and 7 data vaults that are stored on the local
system.
Name Name of the Data Vault.
Database Schema Database schema.
Create… N/A Creates a new local or network Data Vault.
Mount… N/A Mount a dismounted Chromeleon 7 Data Vault.
Chromeleon 6… N/A Mounts a Chromeleon 6 Datasource.
Dismount N/A Removes a Chromeleon 6 or 7 Data Vault.
Upgrade Schema N/A Performs a manual Data Vault schema upgrade.
Configure N/A Configure Multi-User Data Vault (see section 11.8.1.2).
Audit trail... N/A Opens Data Vault Management Audit Trail dialog (see section 12)
Refresh N/A Refreshes display of Data Vaults.
Service Settings... N/A Configure Data Vault service settings (see section 11.8.1.3).
11.8.1.2 Configure Multi-User Data Vault

Multi-user data vault(s) can be configured on the system where the data vault is hosted.

Chromeleon 7


Load balancing server(s) Lists all load balancing servers. Master system is displayed in the first
line of the list. Additional load balancing servers can be added or
removed. The master cannot be removed.
Server Load balancer name.
Type Load balancer type.
Status Load balancer status.
Organizational unit N/A Associate organizational unit that Multi-User Data Vault belongs to.
11.8.1.3 Data Vault Service Settings


Local System N/A The Local System account is a predefined local account of
the operating system.
User Account Domain Domain of user account to be used by data vault service.
User User name to be used by data vault service.
Password This is used to set the logon password for defined user.
Retype Password Confirmation of logon password for user.
This service can be used for load N/A Enables Data Vault service to be used as a load balancer.
balancing

Chromeleon 7
11.9 Configure Discovery

The Discovery Service maintains a central index of various Chromeleon resources (instrument controllers, data vaults, and
clients) that these resources use to maintain awareness of each other and establish communications.
11.9.1 Discovery Configuration
Figure 60: Discovery Service Configuration


Chromeleon Domain Controller N/A The locator control displays the current location and contains a drop text
box and a button to browse for other locations.
Organizational Unit N/A Associate organizational unit that discovery service belongs to.
Notifications (choose at least one) Receive push Clients subscribe to receive notifications about updates to Discovery (on
notifications by default).
Poll for updates every Client machines simply poll the domain controller discovery service for
... sec resource information on a regular interval of x seconds.
Connection Security Require enhanced New certificates for the communication between different Chromeleon
connection security Services and Chromeleon client applications have been introduced in
(Chromeleon 7.2 SR5 order to enhance transport security.
and above) If checked the Chromeleon services will communicate via new Windows
Communication Foundation (WCF) hosts based on a new certificate
created using SHA-256 hash algorithm.
If unchecked the old legacy hosts will be started additionally and enable
clients with Chromeleon versions <7.2 SR5 to connect.

Chromeleon 7
12 Administrative Audit Trails

A common audit trail viewer control/window is used for all of the following audit trail views: Domain Resources, Data Vault
Management, Instrument Configuration, Station, Global Policies, eWorkflow Tags and Organizational Unit Summary.
Figure 61 shows the audit trail viewer control/window.
Figure 61: Administrative Audit Trail

The data audit trail offers the following toolbar controls:
Reload Reloads the data audit trail from the Data Vault.
Report Creates a report of the data audit trail.
Show Changes Opens the details window, if details are available for the selected audit trail record.
From <date> to <date Allows to filter the list to changes made in the given time range.
The audit trail displays the following default columns, but the actual list depends on the context of the audit trail:
Date/Time The date and time when the item were modified.
Operator The user who made the modifications.
Operation The type of modification.
Computer Name The name of the computer from where the modification was made.
Application The name of the application that made the modification.
Application Version The version of the application that made the modification.
Comment Comment entered by the user or the application about the modification.
Additional Information Additional information where available.
Object The modified object.
Org. Unit The organizational unit of the object.
Category The category identifier.
Old Value The value prior to any modification.
New Value The resulting value after any modification.
Object Type The type of object that has been modified.
Host Name Indicates the host name of the computer where a particular resource was running.

Chromeleon 7
13 Time Zone Information

A tooltip provides additional information about time zone offset and how it translates to local machine date time. The tooltip
appears under the mouse pointer when it is hovering over a Date and Time with offset field. The tooltip is available in
ePanels Audit Trail control, Console folder details, Sequence Inject Time and Associated items, Data Vault, Folder and
Injection Properties, and all audit trails.
Figure 62 shows the time zone tooltip.
Figure 62: Time Zone Tooltip

When the mouse pointer is rested over a date and time the following information is displayed:
• The time offset from Coordinated Universal Time (UTC)
• The time offset from your local computer (including any daylight savings time adjustments that apply)
• The conversion of this date and time to your local time zone

Chromeleon 7
14 Changes Introduced in Version
14.1 7.2
3D View 110
Absolute Value 279
Add 12
Adds table 19
Agilent ICF configuration 20
AnDI/NetCDF file format 263
Apply scaling to all plots passim
Arithmetic Combination 95
Available algorithm version 305, 306
Blank Run injection Record 305
CAS 62, 102
Check for Errors 269
Chem. Formula 62, 63, 102
Comparison passim
Consolidated Table 131, 239
Convert 27, 47
CORREL 261
Data Audit Trail 132, 255, 287
Database Statistics 37, 41
Date Modified 18
Deleted Items 26, 36, 42
Derivatives 96
Detection Algorithm 288
Displaying Imported Results 281
Export GAML 340
Export AnDI 340
Extracted Ion Chromatograms 60, 102
Filter Peaks 235
Format 40
GAML file format 263
Grouping 265, 266, 267, 268
Grouping Options 236, 243
Groups 19
GUID 39, 284
Header Rows passim
Hit Mass Spectrum 302
Hit Spectrum 303
Import Non-Chromeleon Data 340
Import Type 288
Imported Data 281
Injection Overlay 186
Injection Rack View 41, 83, 132, 206
Interactive Settings passim
INTERCEPT 261
Label 112, 140
Legend passim
Library Spectral Filter 65, 311
Mass Spectra 83
mass spectral plot 19, 195
Mass Spectrometry 314
Mass Spectrum 289, 302
Metadata 289
Mol. Mass 62, 102
Monitor Baseline 16
MS 93
MS & Results 48
MS Components 83, 201
MS Detection 72
MS Detection Settings 132
MS Device 314
MS Device Information 132, 258
MS Instrument Method (XRAW) 132, 254
MS Library Screening 75, 310

Chromeleon 7
MS Quantitative 82
MS Raw Spectra 131, 243
MS Settings 74, 310
MS Signal Extraction Parameter 290
MS Spectral Library 26, 36, 273
MS Status Log 132, 258
MS Tune Report 132, 254
Network 341
Non-Chromeleon data 10, 14
Options 121, 131
Overlay order 90
Override Access Control 339
Peak Purity and Identification 300, 305
Power Law 97
Proportional 187
Queue Settings 33
Re-injections 39, 285
Report Column passim
Report Mode 279
Result Formula Statistics 39, 40
Round Value 279
Signal Axis 171, 181, 221
Signature Programs 333
SLOPE 261
SmartLink passim
Smooth Channel 97
SQ / QqQ GC-MS Data Acquisition 329
SST/IRC 66
System Suitability IRC 132
Table Channels 235
Test Case Overall Result 286
Test Case Specific Result 286
Tick mark intervals 171, 181, 221
Time mark intervals passim
Trace 1300 command 20
Triggers 91, 185
TriPlus RSH command 20
TriPlus RSH Status 20
Update Detection Algorithm Version 339
14.2 7.2 SR1

Acquisition List 77
Autodilution 66, 69
ChemStation Data Import 15
Composite Scoring 71, 300, 301, 305, 306, 309
Configure Multi-User Data Vault 349
Custom Formulas 269
Custom Formulas Editor 12
Customizable Titles 99, 111, 116, 123, 128
Data Vault Service Settings 350
Discovery Configuration 351
Exponential Function 279
Export MS raw File – new privilege 340
Export MS raw file format 263
Fraction Collection – new license 329
Fraction Tray Pane 133
Fraction Tray Plot 207
Fraction Tubes 92, 185
Fractionation - Fraction Table 258
Fractionation - Tube Table 259
Host Name Resolution 341
Inhibit Integration for TIC 75, 310
LC-MS Data Acquisition – new license 329
Load balancing 350
Logarithm 279

Chromeleon 7
Logarithmic scale for calibration 98, 99

Log-log linear transformation 99
Logon Roles 340
Mass Precision 75
Mass Spectrometer Instrument Methods 44
Modify Custom Formulas – new privilege 340
Modify List of Custom Formulas – new privilege 338
MS Component Table Export 77
Natural Logarithm 279
Number of recent passwords, that cannot be used again 333
Open MS raw file with registered application 28
Organizational Units 335, 336, 337, 341
Password change restriction 335
Password complexity 332
Peak to Valley Ratio 293
Standard Instrument Integration – new license 329
User Report Templates Locations 342
14.3 7.2 SR2

AutoDilution 66
Autoscale in fixed time range 88, 171, 182, 222
Autoscale in time range or peak 88, 171, 181, 221
Autoscale in visible time range 88, 171, 182, 222
Autoscale on peak 88, 171, 182, 222
Calculated Mass 284
CE Area 292
Detection parameter label 93, 156
Errors passim
Exclude users 332
Frame 320
Frame Table 131, 244
Launch 19
Manual commands 91, 185
Manual Commands 93, 172, 187, 223
Manual Injection 338
Method of noise calculation 295, 296
Non-Targeted MS Processing 46, 316
NTMS Chromatogram Plot Pane 162
NTMS Frame Plot Pane 160
NTMS Frame Report Pane 162
NTMS Mass Spectra Pane 163
NTMS Processing Pane 159
NTMS Ribbon Bar 158
Provides embedded PDF 19
QD Calibration 76
QD Quantitative 82
Remove All Manual Assignments 86
Remove Manual/Automatic Assignment 86
Requires Reference Peak 102
Selected peak 93
Selected peak label 93, 156
Signal parameters 91, 185
Time interval for noise calculation 296
TriPlus 100 LS command 20
TriPlus 100 LS status panel 20
14.4 7.2 SR3

AutoFilter Filtering 156
Baseline Corrected 303
Baseline Correction 303
Calibration Levels 57
Chromeleon data file format 263
Chromeleon data files 10

Chromeleon 7
Chromeleon PQ 11
Comment 33, 345
Concentration Level Tolerances 63
Confirming Peak Ion Ratios 61
Copy 153
Create MS Channel 153
Data Range for Extracted Ion Chromatograms 60
Data Range for MS Components 73
Define Policies in Organizational Units 344
Display “QC Sample” for injections of type “Check Standard” 343
eWorkflow Tags 31, 344
Export Chromatogram 153
Extract MS Channel(s) 69, 70
From <date> to <date> 274
Full Scan Mode 79
Include Subfolders 274
Instrument Selection 34
ISQ 78
Level 25, 276
Level Check 285, 293
Level Tolerance High Amount 293
Level Tolerance High Response 293
Level Tolerance Low Amount 293
Level Tolerance Low Response 293
Line & Fill Styles 155
MS AutoFilters 152
Neutral Loss Scan Mode 80
Next Day 25
Next Injection 276
Normalize signal 91, 149, 184, 185
Normalize time 91, 185
Open Chromeleon Studio 35
Peak Characterization 155
Peak Label 155
Plot Details 154
Precursor Ion Scan Mode 79
Previous Day 25
Previous Injection 276
Product Ion Scan Mode 80
Properties 154
QED Scan Mode 79
Relative CE Area 293
Remote Data Vaults 342
Retention Time Standard Peak Area Ratio 53
Run eWorkflow ‘Approved’ 339
Run eWorkflow ‘In Development’ 339
Run eWorkflow ‘Ready’ 339
Run eWorkflow ‘Retired’ 339
sampler positions when the eWorkflow is launched 34
Sampler start position 34
Save only a link to the selected Report Template 32
Save only a link to the selected View Settings 32
Scale 154
Separate Policy Settings for Organizational Units 344
Show Description at Launch 31
Show local Data Vaults of remote systems 342
SIM Scan Mode 79
SRM Scan Mode 78
Tag Name 345
The list of eWorkflows in the navigation area can be grouped and filtered 30
Tolerance [%] 57
Toolbar 331, 341, 344
Troubleshooting 17
Try Launch 34
TSQ Quantiva and TSQ Endura 78
UI Customizations 343
Use <Global> Settings 344
User Mode 345
XICs 61

Chromeleon 7
Zooming and Navigating in the MS AutoFilters pane 152
14.5 7.2 SR5

Access Group List 337
Administrative Audit Trails 352
All Resources 345
All Resources Context Menu 345
Audit trail 349
Audit Trail 331
Bulk Import 14
Chromeleon 6 data files (*.cmb) 14
Chromeleon Consoles 348
Chromeleon Consoles Context Menu 348
cmb 14
Computers 346
Computers Context Menu 346
Connection Security 351
Create Sequence from Injection Query Results 338
Create Sequence via Save As 338
Create Sequence via Save As with Raw Data 338
Data Vault Management Audit Trail 349
Data Vaults 347
Data Vaults Context Menu 347
Default logon role 335, 336
Domain Resources 345
Email Configuration 343
Enable privileged actions 36
Format date/time as text passim
Imports multiples of Chromeleon data files 14
Instruments 348
Instruments Context Menu 348
Last Fixed Calibration Update Date and Time 307
Last Fixed Calibration Update Operator 307
Maintenance Window Settings 346
Manage Maintenance Window 340
Manage Privileged Actions 340
Overwrite Default Comment 340
Privileged Actions 343
Raw Data 344
Reactivate User(s) 334
Retire User(s) 334
Roles List 337
Send email notification when a user account is locked 333
Send email notification when a user signature password is locked 333
Station Audit 343
Time in universal coordinated time passim
Time offset in hours passim
Time using local time zone passim
Time Zone Information 353
Toolbar passim
User List 334
14.6 7.2.6
Amount Ratio for Variable Internal Standard 63
Chromatogram Report Variables 289
Chromeleon XPS Permissions 340
Component Match by Mass Spectrum 54
Detection Settings - Reference Mass Spectrum 59
Electronic Signatures 340
eWorkflow Notification Settings 33
General User Properties 335
Injection Report Variables 284
License Notifications 343

Chromeleon 7
MS Component Table Import 77

MS ComponentsPlot Signal Axis 146
MS Plot - Show Detected Mass Info 140, 198
Password Attempts 333
Sequence Notifications 41
Sequence Table Target Mass Support 39
UI Customizations 343
14.7 7.2.7
Ad Hoc Libraries Search Window – Multiple Library Search Function 120
Autorepeat Areas - Two Repeat Levels 265, 266
Chromatogram Plot Property - MS Quantitation Channel 92, 186
Import - Empower Data 15
MS Component Plot Properties - Reference Injection 147, 149, 201, 204
14.8 7.2.8
Admin Console - Ready for LIMS transfer 333
Cobra Integration - Fixed Baseline 50
Component Table - Context Menu 52
eWorkflow - Auto-reporting Settings 33
Instrument ePanel - Fluidic Configuration 17
Instrument Controller Queue - Enforce Export 326
Instrument Controller Queue - Enforce Print 326
Sequence Properties - Autogenerate Report 41
Sequence Properties - Export 41
Sequence Properties - Print 41
Tentatively Identified Peaks - CAS Number 152
Tentatively Identified Peaks - Add To Component Table 152
Tentatively Identified Peaks - CAS Number 305
User Management - User Account Restrictions 334
XIC Extraction - Include in Calibration 62
14.9 7.2.9
BioPharma Finder Workbook Import 77
Data Processing - Linking Internal Standards 55
Data Processing – Multiple Variable Internal Standards 40, 55
ePanel Control - Instrument Data Browser 19
Execute On-demand Auto tune 338
Export Notification 263
Intact Protein Deconvolution 163
Intact Protein Deconvolution Report Variables 317
IPD Chromatogram Pane 169
IPD Chromatogram Report Object 219
IPD Component Results Pane 167
IPD Component Results Report Table 246
IPD Deconvoluted Spectrum 173
IPD License 329
IPD Mass Deconvoluted Spectra Report Object 223
IPD Mass Source Spectra Report Object 226
IPD Processing Method Pane 164
IPD Processing Parameters Pane 167
IPD Processing Parameters Report Table 248
IPD Ribbon Bar 163
IPD Source Spectrum Pane 176
LIMS transfer 333
Modify When Visible Views are Updated 339
Notifications 263
On-Demand View Updating 158
Peak Grouping - General 57, 58, 292, 308
Peak Grouping - Report Category 308, 312
Peak Grouping - Report Table 131, 249
Peak Grouping - Results 250

Chromeleon 7
Processing Method - Peak Group Table 63

Save Electronic Report 33, 41, 326
System Printers 346, 348
UI Cusomitzations 343
Update Visible Views For MS Data 33, 40
Updater Package 347
Updater Repository 340, 345, 346
14.10 7.2.10
Allotrope Export 263, 340
Autoreporting Settings 41
Bulk Copy XIC Detection Settings 102
Close Client After Inactivity 332
Component Match - New Options 53
Configure Autoreporting 33, 34
Edit Peptide Name 52
Effective Smoothing Width (Cobra) 288
Enforce Print/Export Report 326
Execute MS AutoTune in a Sequence Privilege 338
Execute MS Manual Tune Privilege 338
Injection Specific XIC Detection Settings 102, 288, 339
IPD Chromatogram 220
IPD Processing Parameters Report Table 228
IPD Results Table 169
IPD Source Spectrum 178, 227
Modify Running Sequence Privilege 339
Multiple Component Assignments 86, 237
NTMS Frame Report Variables 320
NTMS Processing Parameters Pane 163
NTMS Processing Parameters Report Table 218, 245
NTMS Processing Setup 159
Peak Highlight 89, 148, 183, 202
QC Check Terminology 343
SmartLink By Injection 156, 158
SmartLink Pane By Injection 118, 125, 142, 150
SmartLink Report Object By Injection passim
Tentatively Identified Peaks 152
TraceFinder compound data store 77
Update XICs Window 61
User Database - Manage Users 336
User Database - Reset Password 335
Versioning - Read-only Studio Window 274
View Settings 47

Functional Specifications - Chromeleon 7.2.10

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1 About this Document 7

4 Objects in the Data Category 36

Functional Specifications Page i

4.4 Injection Query 42

Page ii Functional Specifications

5.5.4 Frame Report Pane 162

7 Chromeleon Variables 279

Functional Specifications Page iii

7.5 Audit Trail 286

8 Electronic Signatures 323

9 Chromeleon Services Manager 325

10 Instrument Configuration Manager 326

Page iv Functional Specifications

10.1.1 Access Control 326

11 Administration Console 328

12 Administrative Audit Trails 352

Functional Specifications Page v

13 Time Zone Information 353

14 Changes Introduced in Version 354

Page vi Functional Specifications

1 About this Document

1.2 Other Documentation

Functional Specifications Page 7

Page 8 Functional Specifications

Figure 1: Overview of the Chromeleon console

1. Category Bars – These provide direct access to

a. Instruments (see section 3.2)

b. Data (see section 3.2.3)

c. eWorkflows (see section 3.4)

a. Local: Items available on the local Chromeleon station.

b. Global: Items available on the Chromeleon Domain.

c. Favorites: Items that have been designated as favorites.

d. Custom: Filter based on text input.

7. The Sequence Status Bar indicates the sequence status.

Functional Specifications Page 9

3.1 Menu Bar

Function Sub Function Description

Administration Console See 3.1.5

Preferences See 3.1.6

Page 10 Functional Specifications

Function Sub Function Description

3.1.1 Station Qualification

3.1.2 Instrument Qualification

3.1.3 Custom Variables Editor

Variable Sub Function Description

Functional Specifications Page 11

Variable Sub Function Description

3.1.4 Custom Formulas Editor

Variable Sub Function Description

3.1.5 Administration Console

Page 12 Functional Specifications

Variable Sub Function Description

3.1.7 Virtual Column Separation Simulator

Figure 2: Virtual Column Separation Simulator

Functional Specifications Page 13

Variable Sub Function Description

3.1.8.1 Chromeleon Data

3.1.8.2 Bulk Import

Page 14 Functional Specifications