CLARITY DEMO

Clarity Demo Software ENG

Code/Rev.: M003/80J
Date: 10/27/2022

DataApex Ltd.
Phone: +420 251 013 400 Petrzilkova 2583/13
[email protected] 158 00 Prague 5
www.dataapex.com The Czech Republic
Clarity ® , DataApex ® and ® are trademarks of DataApex Ltd. Microsoft ® and Windows TM are
trademarks of Microsoft Corporation.
DataApex reserves the right to make changes to manuals without prior notice. Updated manuals can be
downloaded from www.dataapex.com.

Author: MP
Clarity Demo Table of Contents

Contents
1 Brief description of Clarity station 1
1.1 DEMO version properties 1
1.2 Hardware and software requirements 2
2 Key features 3
2.1 Control Modules 4
2.2 Clarity Extensions 4
3 Clarity Demo version installation 6
4 Program structure and control 7
5 Tour through the Clarity station 9
6 Running the Single Analysis 10
6.1 Instrument window 10
6.2 Single Analysis dialog 12
6.3 Data Acquisition window 14
6.4 Chromatogram window 16
7 Running the Sequence measurement 18
7.1 Sequence window 18
7.2 Calibration window 20
7.3 Linking the calibration to a chromatogram 24
7.4 Linking the calibration to the method 25
7.5 Linking the calibration to a series of already measured chromatograms 25
8 Alternative demo projects 28
8.1 Demo GPC Project 29
8.2 Demo PDA Project 29
8.3 Demo NGA Project 29
8.4 Demo EA Project 30
8.5 Demo DHA Project 30
8.6 Demo MS Project 31
8.7 Demo GCxGC Project 31

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Clarity Demo Table of Contents

To facilitate the orientation in the Clarity Demo manual and Clarity chromatography station,
different fonts are used throughout the manual. Meanings of these fonts are:
Instrument (blue text) marks the name of the window to which the text refers.
Open File (italics) describes the commands and names of fields in Clarity, parameters that can
be entered into them or a window or dialog name (when you already are in the topic describing
the window).
WORK1 (capitals) indicates the name of the file and/or directory.
ACTIVE (capital italics) marks the state of the station or its part.
The bold text is sometimes also used for important parts of the text and the name of the Clarity
station. Moreover, some sections are written in format other than normal text. These sections are
formatted as follows:

Note: Notifies the reader of relevant information.

Caution: Warns the user of possibly dangerous or very important information.

▌ Marks the problem statement or trouble question.

Description: Presents more detailed information on the problem, describes its causes,
etc.
Solution: Marks the response to the question, presents a procedure how to remove it.

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Clarity Demo 1 Brief description of Clarity station

1 Brief description of Clarity station

This Guide is suggested for walk-through the Clarity Demo.

The Clarity chromatography station is an effective tool for the acquisition,
processing and evaluation of data. It permits the collection of data from
virtually any gas or liquid chromatograph. It is possible to measure on up
to four chromatographs simultaneously, of which each may be equipped
with up to 32 detectors. Each chromatograph may use further add-ons
such as Extensions (e.g. CE, EA, GPC, GCxGC, MS...) and Controls (LC,
GC , AS control...). Clarity supports the requirements of the FDA’s 21
CFR Part 11 guidelines.
It is possible to obtain the Clarity Lite Demo station which does not
contain same functions and DEMO examples as is described in this guide
for the full version of Clarity Demo . For complete overview of the
differences, please see D007 datasheet: Clarity x Clarity Lite
Comparison Table which can be obtained from DataApex Downoalds at
our website (www.dataapex.com/downloads).

1.1 DEMO version properties

The DEMO version which you have received, contains all functions of the
full version with the following limitations:
Not possible to control instruments.
Not possible to acquire real data.
Not possible to import chromatograms.
“DEMO” inscription in the header of the main Clarity window and on all
printed documents.
The Clarity Demo version allows you to try data acquisition procedures
even without the converter board because the necessary data are
simulated by data files.
The Clarity Demo station uses only what is known as “demo data”, it
cannot process or import real chromatograms.
If you want to try the evaluation of your data, please let us know at
[email protected]. We can prepare Clarity ready chromatograms from
AIA FILES (*.CDF) your chromatograms.
Following ASCII text files containing signal values can also be supplied:
Multidetector files (*.chr)
Text files (*.txt)
Comma separated values (*.csv)
EZChrom ASCII files (*.asc)

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Clarity Demo 1 Brief description of Clarity station

1.2 Hardware and software requirements

The Clarity station will operate with any of the following Microsoft
Windows systems (in any language): 7 SP1 , 8.1, 10 and 11 and supported
are also the 64-bit versions.
Recommended PC configuration is PC Pentium 4/2 GHz and newer, 4GB
RAM. Minimal is Pentium 4, 2GB RAM.
We recommend monitor resolution 1280x1024 or 1680x1050, 64K (16 bit
High color). The minimum requirement is 1024×768 pixels with 64K (16
bit – High Color).
Clarity installation requires Microsoft .NET framework version 4.7.2 or
higher.
For more details, see Clarity Compatibility Table datasheet (D016 – for
download from www.dataapex.com/downloads).
Typical installation requires approx. 1GB of free HDD/SSD space.
Minimal requirement is at least of 350 MB and Full installation requires up
to 1.2 GB.

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Clarity Demo 2 Key features

2 Key features
Measuring - Simultaneous data acquisition from up to four 32-detector
chromatographs (4×32 configuration).
Integration - There are extensive possibilities for modifying
chromatograms. The chromatogram can be changed by entering global
parameters or interactively, through the direct graphical modification of the
baseline.
Overlay - Simultaneously displays a virtually unlimited number of
chromatograms and their mathematical modification, for example, mutual
deductions or derivations of any order.
Calibration - Internal and external standard calculation methods,
calibration of groups of peaks and reference peaks for better identification.
Automated measuring support - Sequence tables for any set of samples
with or without an autosampler.
Postrun - Automatically displays, prints, exports and starts other programs
after completion of measurement.
Summary result tables - Displays and prints selected results from all
simultaneously displayed chromatograms.
User settings - User selects parameters for peak display and the
specification for axes, including color from an extensive array of color
settings. Text labels and lines, either as part of the area or anchored to a
chromatogram, may also be inserted.
Export - Optional export of all results with or without the chromatogram, in
various formats, into a file or clipboard.
Import - Imports chromatograms or mathematical curves, which have
been saved in text or AIA formats, from other programs.
Method and calibration history - Each chromatogram can easily be
displayed under the same conditions as when it was printed, exported or
saved.
Column performance - Calculations of peaks in terms of symmetry,
efficiency, resolution; all by several methods (tangent, moments, etc.).
Batch - Automatically batch processes, displays, exports or prints any
number of chromatograms.
User calculations - User can define custom calculations in the Result and
Summary tables. Using the integrated editor you can create your own
columns from the original columns and individual mathematical functions.
User accounts - Sets up access rights and passwords (including their
parameters, e.g., minimum length, validity, etc.). Each user can define his
or her own station appearance.
Audit trail - Records selected events and operations into a special file.
Records selected operations directly into a chromatogram.
Electronic signature - Each chromatogram can be electronically signed.
Signature selection is based on the username or the signature certificate.

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Clarity Demo 2 Key features

2.1 Control Modules

Software modules that provide an interface for chromatography devices
such as GC and HPLC systems, Autosamplers, Fraction Collectors and
Valves. Direct control allows the device(s) to be controlled and monitored
from the Clarity environment. The instrument method that controls the
device is saved in the measured chromatograms.

2.2 Clarity Extensions

Software modules that enhance the capabilities of the Clarity data station.
Extensions provide features within Clarity that are specific to a given type
of analysis or for a specific task. Currently available modules are:
l SST (System Suitability Test) - Integrated module for monitoring the
quality of a measurement.
l GPC - Integrated module for performing and evaluating GPC/SEC
analyses (GPC = Gel Permeating Chromatography , SEC = Size
Exclusion Chromatography).
To review the GPC Extension open Instrument My GPC.
l PDA - Integrated module for evaluating analyses from PDA (Photo-Diode
Array, also called DAD - Diode Array Detectors).
To review the PDA Extension open Instrument Agilent 1100 with DAD.
l CE - Integrated module for performing and evaluating analyses from
Capillary Electrophoresis. Brings CE terminology to Clarity.
l NGA (Natural Gas Analysis) - Integrated module for evaluating the
calculations according to selected norms in analyses of natural gases and
liquefied petroleum gases.
To review the NGA Extension refer to chapter 8 - Alternative demo
projects.
l EA - Integrated module for performing and evaluating Elemental
Analyses.
To review the EA Extension refer to chapter 8 - Alternative demo
projects.
l DHA - (Detailed Hydrocarbon Analysis) - Integrated module for
determination of individual components in spark ignition engine fuels
(PIONA, etc.).
To review the DHA Extension refer to chapter 8 - Alternative demo
projects.
l MS (Mass Spectrometry) - Integrated module for evaluating analyses from
MS detectors.
To review the MS Extension refer to chapter 8 - Alternative demo
projects.

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Clarity Demo 2 Key features

l GCxGC - Integrated module for interactive analysis and compound

identification in chromatograms measured on any gas chromatograph
equipped by two columns and a modulator.
This Extension is accessible only after Full installation of Clarity Demo.
The installation procedure is described in 3 - Clarity Demo version
installation.
To review the GC x GC Extension refer to chapter 8 - Alternative demo
projects.

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Clarity Demo 3 Clarity Demo version installation

3 Clarity Demo version installation

The Clarity Demo can be acquired in two ways - either on the USB or
downloaded from the www.dataapex.com/downloads.
In case of the Clarity Demo USB:
Plug in the USB.
Run the INSTALL.EXE file.
In case of downloaded version:
Download the Clarity Demo version.
If the installation does not start automatically, double click the
downloaded INSTALL.EXE file.
The installation wizard will guide you through the entire installation. After
selecting the destination directory, an option of Typical , Custom or Full
installation is to be made.
You can simply select Typical and follow the instructions of the installation
wizard until the entire installation is completed.

Note: Typical installation will provide all of the components needed for a
successful DEMO operation, although some of the control modules will be
absent. Custom installation can be used for selection of files to install.

Caution: It is recommended to uninstall any previous installation of Clarity Demo

and in the installation wizard select Overwrite all files without asking to be
able to follow this manual in the chapter "Tour through the Clarity
station" on pg 9.
After installing the software, the installer will create a Clarity Demo

shortcut in the Start - Programs menu and a Clarity Demo icon on the
desktop. During the installation was created a System configuration with
predefined configuration for 4 instruments offering review of GC with
autosampler control, LC control, GPC Extension and DAD Extension.
Refer to following image.

Fig 1: Clarity Demo

To review other Clarity Extensions and projects refer to the chapter

"Alternative demo projects" on pg 28.

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Clarity Demo 4 Program structure and control

4 Program structure and control

Clarity software has a hierarchic structure. After start-up the main Clarity
window will be displayed with the symbols of configured Instruments.
After clicking on the chromatograph picture and entering the User Name
(more information on User Names can be found in the Reference Guide)
the Instrument window will be displayed. This window is used for
acquisition and processing of data using the connected chromatograph.

Fig 2: Clarity and Instrument windows

Note: The Clarity station works with so- called Instruments. All detectors
connected to the same Instrument share a common time base.
The main Clarity window is designed to set the station’s configuration,
select access rights and basic directories for saving data.
The Instrument window is used for measuring and evaluating an analysis
from a selected chromatograph. The window is displayed by clicking on
the symbol of the relevant chromatograph in the station’s main Clarity

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Clarity Demo 4 Program structure and control
window. Depending on the number of the Instruments, up to four
independent Instrument windows can be displayed.
Each Instrument window contains an information table ① , status line ② ,
analysis-processing diagram ③ and instrument image ④. Instruments are
distinguished by line color in the analysis- processing diagram and
Instrument name in the header.
All dialogs relevant for performance of actions in the Instrument window
can be easily accessed from the Instrument window by using appropriate
commands from the menu or by clicking on their icons.
Note: In Tablet mode, processing icon's text description is not visible. Window
invoked from Instrument window is indicated by blue frame around the
icon.

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Clarity Demo 5 Tour through the Clarity station

5 Tour through the Clarity station

The following two sections will show you, step by step, the process of
performing a single analysis (the chapter "Running the Single Analysis"
on pg 10 . ) and sequence measurement ( the chapter "Running the
Sequence measurement" on pg 18 .). These chapters are shown as a
succession of steps, from which all should be performed in the given
order. Some sections may be skipped, as we prepared their output for you
to be used later. You will be notified of such sections. Also, the whole
process presents Notes - the procedures described in them are optional
and you don’t need to perform them in order to reach the goal.
The Clarity software is intuitive and easy to master even without
excessive training. The first analysis can be run in less than one minute
after installing the station and configuring the hardware.
This tour is primarily designed for the users who installed the Clarity
Demo version.
Note: Although this is only a tour of the station aimed at beginners with Clarity, it
assumes users have basic knowledge specific to chromatography
principles and basic processes such as calibration.

Note: When in doubts, pressing the F1 key or Help button shows help page
concerning the specific window or dialog. In the invoked help, the Index
tab serves for keywords searching, whereas the Search tab serves for
fulltext searching.

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Clarity Demo 6 Running the Single Analysis

6 Running the Single Analysis

There is a simple project aimed on basic functions prepared on the
Instrument 2 (labeled My LC). It shows the way to start a Single Analysis,
monitor the Data Acquisition and process the resulting Chromatogram.

6.1 Instrument window

Start the Clarity Demo station. The Clarity main window will display,
showing four configured Instruments.
Open the second Instrument (labeled My LC) by clicking on its icon. Login
Dialog will open. Choose the Project DEMO2.
Administrator user name is pre- selected. This User Account needs no
password, thus proceed by pressing the OK button. The dialog about
Method Setup adaptation may be displayed. Press Yes and adapt the
Method in the Method Setup dialog. In case you are using Demo2 project,
just click on the OK. Alternatively you can press Help to learn more about
method adaptation. Now the Instrument window will be displayed.

Note: You can create your own User accounts from the main Clarity window
using the System - User Accounts... command.

Fig 3: Instrument window

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Clarity Demo 6 Running the Single Analysis
The Instrument window will open; Fig 3 on pg 10 . shows the most
important icons in this window. During the tour, we will present all
windows related to these icons.

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Clarity Demo 6 Running the Single Analysis

6.2 Single Analysis dialog

Use the Single Analysis icon in the Instrument window to open the
Single Analysis dialog.

Fig 4: Single Analysis dialog

Fields in the Analysis section carry the information about the sample. All
necessary parameters are already set for you, but we will browse through
them nonetheless.
Sample ID and Sample fields ① are purely informational, whereas the
data in Amount, Dilution, ISTD Amount and Inj. Volume fields ② are used
for further calculations.
Choosing the Standard from the Sample Type combobox and entering a
value in the Level field ③ would mark this sample as the calibration
standard and save the chromatogram into the CALIB subdirectory.
The measurement of the sample will be performed according to the actual
modification of the template method opened in the Instrument window.
The Edit Method... button ④ serves to change the parameters of the actual
template method. Click the button to open the Method Setup dialog and
check the setting of the Autostop parameter (Autostop is enabled and Run
Time is set to 7.5 minutes). Return to the Single Analysis dialog by
pressing OK button.

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Clarity Demo 6 Running the Single Analysis
The Chromatogram File Name field ⑤ serves to enter the file name of the
resulting chromatograms. It is possible to use rigid text together with
variables adding the time, date, sample name or other parameters to
create unique chromatogram name. The resulting name can be seen just
above the field ⑥ in parentheses.

Note: The complete set of available variables can be seen after clicking on the
field and selecting the icon.
Run the analysis by clicking the Run button ⑦. The Single Analysis dialog
will close now, but if you open it again, you will see three more buttons
( Stop , Abort, Snapshot) accessible, allowing you to stop or abort the
analysis or take snapshots (see the chapter "Data Acquisition window"
on pg 14.).
Close the Single Analysis dialog and return to the Instrument window.

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Clarity Demo 6 Running the Single Analysis

6.3 Data Acquisition window

In the Instrument window, look at the Status line (see Fig 3 on pg 10.). The
acquisition is now signaled by the RUNNING state and the actual run time
is displayed there.
To see the data acquisition in process and possibly control it, use the Data
Acquisition icon (see Fig 3 on pg 10 .) to enter the Data Acquisition
window.
In the Data Acquisition window two signals can be seen. This is because
the analysis is set as two-detector ① analysis.

Fig 5: Data Acquisition window

In the Status bar on the bottom of the Data Acquisition window, the time of
the analysis ② can be seen, as well as the signal for each detector ③ in
its particular units.

Note: If the detector range exceeds the tolerance limit by ± 1.285%, the OVER
string in red lettering will be displayed in the part of the status bar
corresponding to the detector.

Stop and Abort icons ④ allow for canceling the analysis. In the
case of stopping, Clarity will save all data acquired so far and cancel the
analysis, while aborting cancels the acquisition without saving any data.
Snapshot icon is also available for creating the preview of already
measured data. After clicking it, the Chromatogram window will open with
the chromatogram file corresponding to the part of the data already
measured (more information on the Chromatogram window can be found
in the chapter "Chromatogram window" on pg 16 .). If the Snapshot
chromatogram is to be preserved, it must be saved under a different
name (File\Save As), as it would be overwritten by the real chromatogram
at the end of the analysis.

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Clarity Demo 6 Running the Single Analysis
After 7 minutes 30 seconds (the time set in the template method used for
the measurement), the analysis will automatically stop and the
Chromatogram window will open.

Note: You can stop current analysis anytime by pressing the Stop or Abort ④
icons
The Chromatogram window opens because the station is set to do so.
These settings are available in the Single Run window at Post Run
Settings tab. Other post run actions including export of data or running
external program can be set there as well.

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Clarity Demo 6 Running the Single Analysis

6.4 Chromatogram window

The Chromatogram window can also be opened manually by clicking on
the Chromatogram icon in the Instrument window.
The Chromatogram window is divided into two halves: the Graph panel
and the Results panel.
Enlarge any part of the graph by selecting the area to enlarge while
holding the left mouse button. Return to the view of the entire
chromatogram by double-clicking in the graph.

Fig 6: Chromatogram window

Only one signal of the chromatogram can be active at a time. The active
signal can be recognized from the legend section ① in the upper right
corner of the graph (active signal is set in bold), from the icons in the
Overlay toolbar ② (the active signal has the highlighted icon) or from
the graph outline color and table headers color. Values inside the tables
change by changing the active signal.
Change the active signal by double clicking on its name in the legend
section ① . Change the color of the currently active signal to another one

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Clarity Demo 6 Running the Single Analysis

by clicking on the Not used color icon in the Overlay toolbar. All parts
of the Chromatogram window mentioned in the previous step will change
color. Return to the former active signal by clicking on its (now raised )
icon in the Overlay toolbar ②.
Click on any row in the Result table ③ . The peak (or peaks)
corresponding to the row you just clicked onto will change color according
to the color of the signal. This change will last until the focus in the Result
table is canceled.
To add permanent color to the peak, click the View button ④ in the right
side of the Results tab. This will get you to the linked calibration file.
There, in the Calibration Summary Table, find the Peak Color column (see
Fig 9 on pg 22.). In the row corresponding to the peak to be colored select
the appropriate color and click OK. Return to the Chromatogram window
by using the icon in the menu. The selected peak is now colored
according to the color selected in the Calibration window.
You can change the integration of peaks by using the interactive icons on
the toolbars on the left side of the Chromatogram window ⑤ or directly on
the Integration tab ⑥ . Any changes made either way will change the
Integration table and can be copied to the template method. To do so,
click on Method - Save as Template... menu comand.

Note: If you want to measure chromatograms with altered integration table,

copy the Integration table and paste it into the template method. New
chromatograms will be automatically integrated according to these
changed parameters. Already measured results can be reprocessed (for
more details see the chapter Linking the calibration to the method
on pg 25).
Before you proceed to work with Instrument 1 (My GC+AS), close the
window of Instrument 2 (My LC). It is not mandatory, but it will be less
confusing to work with one Instrument at a time only. You will be asked to
save any unsaved files.

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Clarity Demo 7 Running the Sequence measurement

7 Running the Sequence measurement

Sequence operation allows automated measurement of large number of
samples for chromatographs equipped with autosamplers. Clarity
provides the possibility to select an ACTIVE (start controlled by the station)
or PASSIVE (start controlled by the autosampler) sequence. It is also
possible to re-process already measured sequences.
Note: It is not necessary to have the AS Control module to use the
autosampler; start synchronization can be performed even without it.
However, the control module can add direct control from Clarity for
automated sending of vial positions, injection volumes, etc., without the
need to program the AS itself.
This chapter and the Clarity demo project prepared on the Instrument 1
will lead you through Sequence, Calibration and Method Setup windows
used for automated measurement and preparation of template methods.

7.1 Sequence window

In the main Clarity window, open Instrument 1 (With the label My GC+AS).
In the displayed Login dialog with the pre- selected Administrator user,
click the OK button.
Use the Sequence button in the Instrument window to enter the
Sequence window.

Fig 7: Sequence window

Look at the Sequence Table. Each row of this table defines one or more
analyses, depending on fields SV (Starting vial), EV (Ending vial) and I/V
(Injections per vial) ①. As it can be seen, the first four rows each present a
single measurement ( SV and EV is the same, I/V is 1 ), while row 5
represents eight analyses (SV is 5, EV is 8, thus measuring 4 samples
from 4 successive vials, and I/V parameter is 2 - each sample will be
measured twice).

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Clarity Demo 7 Running the Sequence measurement
Also, note that in the Sample Type and Lvl fields ② the first four samples
are marked as standards on levels 1-4. These will be used for automatic
making of the calibration (or its recalibration, if there already were any
data in the calibration).
The Method Name column ③ sets the template method used for
measuring the sample. The Report Style column ④ sets the print style
used for reporting the measurement. Each row can have its own template
method and report style; it is thus possible to measure according to
several template methods in one sequence.
In the File Name column ⑤ , the name of the resulting chromatogram file
is specified. It is possible to use variable parameters to form the
chromatogram filename, for example %Q means that the file name will
use the text from the Sample field. It is possible to combine several of
these variables with hard-set text or symbols to create a unique file name
for each chromatogram. The complete set of available variables can be
seen after clicking the field and selecting the icon.
To check the sequence, press the icon ⑥ . Clarity station will keep all
symbols at the beginning of the row green ( ) meaning the row is
ready or issue an error/warning message listing what should be
corrected on which row to be able to proceed.

Note: For demonstration purposes only, try to make a mistake and check the
sequence once more. For example, on row number 3, change the text in
the Sample column to Std_1, you can see immediately that a warning sign
appeared on the corresponding rows - 1 and 3. After pressing the icon,
warning message appears telling that there are two rows which would
produce chromatogram with the same file name. Holding the mouse
above either field will display the tooltip with the cause of the problem. Set
the sequence back to its original state and continue to the next step.

Start measuring the sequence using the icon ⑦ . The state of the
ACTIVE sequence will change to WAITING FOR READY and as soon as
the Ready signal from the autosampler is detected, the measurement will
start.

Note: Even if the autosampler is not connected, Clarity Demo will get the
Ready signal, thus starting the sequence. However, it is not possible to
give its own demo data for each chromatogram, so all chromatograms
would be the same. All files are already prepared for you. You may stop or
abort the sequence now or later either from the Data Acquisition window
or directly from the Sequence window.
After the first row of the Sequence table (controlling one analysis) is
measured, the Instrument will once again switch to the WAITING FOR
READY state and the autosampler will start a new measurement by
sending the Ready signal. Stop the sequence from the Data Acquisition

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Clarity Demo 7 Running the Sequence measurement

window or Sequence window at any time by pressing the Stop button

(single-click means that the currently measured Chromatogram will finish
and the sequence will stop subsequently, after double-click the sequence
will stop immediately). All data measured will be saved. Or abort the
measurement with Abort button (does not produce any chromatogram
).
Already measured rows will change Status from green field ( ) to icon
with small chromatogram ( ). If there is a chromatogram resulting
from this row, small triangle will appear in the icon - . Left mouse
click on the triangle will reveal option to open the chromatogram(s). You
can click on the name of the chromatogram to open it or select option to
open all chromatograms in overlay.

Note: It is possible to edit the sequence even during the measurement.

On the right side of the Sequence Window you can check at each row
whether corresponding chromatogram should be opened, printed or
loaded into the calibration window.

7.2 Calibration window

The following section describes how to make a calibration.
Use the Calibration button in the Instrument window to open the
Calibration window.

Note: If you wish to skip the following section about creating a new calibration,
you can open (via the File - Open... command) the calibration file
DEMO1.CAL we prepared for you instead and test the functions of the
Calibration window on it. In this case you can continue with the chapter
"Linking the calibration to a chromatogram" on pg 24.

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Clarity Demo 7 Running the Sequence measurement

Fig 8: Calibration window - empty

It is necessary to create a new calibration. Use the New Calibration

icon ① to create new calibration file. Save the calibration under
CALIBDEMO for example.

Note: To save the calibration now, it would be necessary to change its name (no
calibration can be saved under the name NONAME.CAL) and fill in at
least the first compound name. Then the calibration can be saved using
the Save Calibration icon ② , File - Save or File - Save As... command.

Use the Calibration Options icon ③ and change the Display Mode (top
right corner of the dialog) to ISTD, then press OK button.
Now, the calibration standards have to be imported to the calibration. Use
the Open Standard icon (yellow) ④ to open the STD 1.PRM data file.
The lower part of the Calibration window now displays the chromatogram
of the calibration standard.

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Clarity Demo 7 Running the Sequence measurement

Fig 9: Calibration window - loaded standard

Check that the Current Level field ⑨ is set to 1 in order to set the
calibration level number 1. Use the Add All icon (blue) ⑤ to move all
identified peaks to the calibration table. The Calibration table appears in
the Calibration window, ready to be completed as seen on Fig 9 on pg 22.
As it can be clearly seen in the calibration, particular peaks are now
identified according to their retention times only. Click and edit the fields in
the Compound Name column ⑥ to those seen on Fig 9 on pg 22. You
may also set the peak color for some peak, for example the ISTD peak, in
the Peak Color column.
Fill the Amount column ⑦ with the concentration of the particular
compounds. In this standard mixture, all compounds except for the peak
number 6 have concentration of 0.4.
Peak number 6 is marked as an ISTD peak. In the Is ISTD column, change
its type to ISTD1 ⑧ and then set its amount in the Amount column to 2.
The first calibration level is now set. On the tabs of the individual
compounds ⑩ (named according to the Compound Name field) the graph
with single-point linear calibration can be seen.
Proceed to setting the other calibration levels. The operation is quite
simple and straightforward - use the Open Standard icon (yellow) ④
again to open another calibration standard named STD 2.PRM. Set the
calibration level in the Current Level field ⑨ to 2 and use the Add All
icon (blue) ⑤ . Fill in the Amount column with 1.0 values (except for the
ISTD peak, in which the 2 value should be used again).
Set the third calibration level accordingly using the STD 3.PRM file and
Amount of 3.0 and the fourth level (file STD 4.PRM, Amount 5.0) except for
the ISTD peak ( Amount 2 every time). On the tabs of the individual

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Clarity Demo 7 Running the Sequence measurement
compounds ⑩ , the linear four-point calibration can be seen. Save the
calibration file now using the Save Calibration icon ② under the name
CALIBDEMO.CAL into the default directory.

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Clarity Demo 7 Running the Sequence measurement

7.3 Linking the calibration to a chromatogram

Any chromatogram can be linked to a calibration file, thus automatically
giving calibrated results. In the Instrument window, use the Chromatogram
icon to open the Chromatogram window.
Use the Open Chromatogram icon to open chromatogram data based
on the calibration you have just created. Use the SAMPLE_VIAL_6-1.PRM
file saved in the default directory. Other files in the directory are
uncalibrated too, but they will be used later.
The data are uncalibrated and no information about the names of
individual compounds is available, peaks in the Result Table are just
described according to their retention times. To change this, the
appropriate calibration should be linked to this chromatogram.
Select the Results tab and look at the section on the right side of the
screen. Use the Set... button in the Calibration File (Peak Table) section to
select the calibration file ( CALIBDEMO.CAL ) created in the previous
chapter. Any peaks present in calibration are now identified with their
names.

Note: In case you skipped the process of making your own calibration, please
use the pre-prepared DEMO1.CAL instead of CALIBDEMO.CAL.

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Clarity Demo 7 Running the Sequence measurement

7.4 Linking the calibration to the method

In case of large number of chromatograms, linking the calibration to each
file separately would be a time- consuming process. To avoid this, the
calibration may be linked to the resulting chromatograms automatically.
Return to the Instrument window and Click on the Method - Calculation
menu command to open the Method Setup dialog directly on the
Calculation tab ① . Alternatively, you can use other comands such as the

Integration , Measurement or Acquisition . All of these sections

(and some others) are part of the template method; thus they are present
within the same dialog but on different tabs.

Fig 10: Method Setup - Calculation dialog

Use the Set... button ② to select the calibration file and link it to the
method.
Exit the Method Setup dialog using the OK button. Clicking this button
applies and saves this change to the template method.
Any chromatograms measured with this template method in the future will
have the actual calibration linked.

7.5 Linking the calibration to a series of already measured

chromatograms
In case you have already measured chromatograms and you want to
change/update the calibration linked to it, it can be done with a single click

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Clarity Demo 7 Running the Sequence measurement
using the Batch reprocess.
This command is especially useful when you have large number of
already measured chromatograms and you want to modify them
somehow.
Steps below will describe how to change the calibration in already
measured chromatograms.
Go to the Instrument window and use the Analysis - Batch command.

Fig 11: Batch dialog with selected chromatograms

Select files to be reprocessed in the left part of the dialog ①; multiple files
can be selected by left-clicking them while holding the Ctrl or Shift key.
Mark all files with the names SAMPLE_VIAL_X-Y in the DATA directory to
be reprocessed, check the Reprocess by Method ② checkbox and click
the Proceed ③ button. All selected chromatograms will now have the
calibration, according to the current method, linked to it.

Note: Chromatograms to be batch processed need to be saved in the current

project directory.
Open the Chromatogram window and load any reprocessed file (e.g.
SAMPLE_VIAL_7-2.PRM) and look at the Result table. All peaks present
in the calibration are now identified and calibrated.
Multiple chromatograms may be displayed at once. Switch to the Overlay
mode by pressing the Overlay button found on the Overlay toolbar (no.
⑦ in the Fig "Chromatogram window") and then use the File - Open
Chromatogram command or the Open Chromatogram icon. It is now

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Clarity Demo 7 Running the Sequence measurement
possible to select several files to be opened in the Open Chromatogram
dialog.

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Clarity Demo 8 Alternative demo projects

8 Alternative demo projects

Clarity Demo opens with four default projects: GC, LC, GPC and PDA.
The GC and LC projects have been described in previous chapters of this
manual. Additionally there are projects EA (Elemental Analysis ), NGA
( Natural Gas Analysis ), DHA ( Detailed Hydrocarbon Analysis ), MS
( Mass Spectrometry ) and GCxGC ( Two- dimensional Gas
Chromatography).
To review the additional projects use:
Launch Manager to set Clarity Demo to corresponding state.
Refer to the corresponding manual that you can find
on the Installation USB media (All Clarity Manuals/Extensions)
download from our website www.dataapex.com/downloads
Launch Manager
Invoke the Launch Manager① available in the Windows Start Menu .
The Select Clarity Profile dialog will open.
Select the desired project and click the Launch button ②.

Fig 12: Start Menu

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Clarity Demo 8 Alternative demo projects

Fig 13: Launch Manager

8.1 Demo GPC Project

The abbreviation GPC stands for the Gel Permeation Chromatography
(also called SEC - Size Exclusion Chromatography). The Clarity station
provides the means to perform the GPC analyses with several modes of
calibration (Narrow, Broad, Broad on Narrow).
The project on the Instrument 3 (labeled My GPC ) allows to test the
capabilities of the Clarity station with the GPC Extension. Twenty
chromatograms and five calibration files are prepared for testing. For more
information on the functions of the GPC module, see the GPC Extension
manual (downloadable at www.dataapex.com).

8.2 Demo PDA Project

Clarity station is able to handle data collected from PDA (Photo Diode
Array) detectors, sometimes also called DAD (Diode Array Detectors).
The third dimension of the spectral data can be displayed in a number of
ways, including 3D rendering.
The project on the Instrument 4 (labeled Agilent 1100 with DAD) enables
to test the capabilities of the Clarity station with the PDA Extension.
Several chromatograms and two calibrations are prepared for testing. For
more information on the functions of the PDA module, see the PDA
Extension manual (downloadable at www.dataapex.com).

8.3 Demo NGA Project

Clarity station can contain a software module called NGA (Natural Gas
Analysis) for Natural Gas and Liquified Petroleum Gas data processing.
You no longer need an external tool for gas properties calculations since
the Clarity contains the complete workflow of data acquisition, peak
calibration, gas properties calculations based on supported norms and
reporting. It is possible to perform summary calculations of gas properties

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Clarity Demo 8 Alternative demo projects
from multiple signals and chromatograms. Calculations in the NGA
Extension currently supports these forms:
Natural Gas
ISO 6976-95
ASTM D 3588-98
GPA 2172-09
Liquified Petroleum Gas
ASTM D 2421-02
ASTM D 2598-02
ISO 8973-97 / EN589-04
The project (instrument labeled as NGA) enables to test the capabilities of
the Clarity station with the NGA Extension. Two chromatograms and one
calibration are prepared for testing. For more information on the functions
of the NGA module, see the NGA Extension manual (downloadable at
www.dataapex.com).

8.4 Demo EA Project

Clarity station can contain a software module called EA ( Elemental
Analysis) for determining the Carbon, Hydrogen, Nitrogen, Oxygen, and
Sulphur (CHNS-O) content of unknowns that is one of the most basic and
essential needs of any chemist. EA Extension provides a simplified
version of the Clarity user interface that speeds up the workflow with
elemental analyzers equipped by autosamplers. EA Extension is an
optional addition to Clarity software, it cannot be used as a standalone
program. Its user interface is optimized for maximum efficiency in
repetitive tasks. Using features that are specific to EA Analysis, such as
Standard Table, automatic weight input from analytical balance and other
improvements, EA Extension provides an interactive and automated tool
for determining the Carbon, Hydrogen, Nitrogen, Oxygen, and Sulfur
(CHNS-O) content of unknowns.
The project (instrument labeled as EA) enables to test the capabilities of
the Clarity station with the EA Extension. Several chromatograms and
one calibration and a sequence are prepared for testing. For more
information on the functions of the EA module, see the EA Extension
manual (downloadable at www.dataapex.com).

8.5 Demo DHA Project

Clarity station can contain a software module called DHA (Detailed Gas
Analysis) for Detailed Hydrocarbon Analysis. It allows the determination
of individual components in spark ignition engine fuels. Clarity brings you
the ability to calculate the properties of the samples directly in the data
station with the complete workflow of data acquisition, peak calibration,
DHA calculations based on supported norms and reporting. These
methods are often referred to as PONA, PIONA, O-PONA, etc. It is possible

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Clarity Demo 8 Alternative demo projects
to create a custom norm which will meet the conditions in your laboratory.
Calculations in the DHA Extension currently supports these forms:
ASTM D-6730
Custom Method - Allows you to create custom norm which will meet the
conditions in your laboratory.
The project (instrument labeled as DHA) enables to test the capabilities of
the Clarity station with the DHA Extension. Several chromatograms and
two calibrations are prepared for testing. For more information on the
functions of the DHA module, see the DHA Extension manual
(downloadable at www.dataapex.com).

8.6 Demo MS Project

The Clarity MS (Mass Spectrometry) Extension is a tool that is used for
processing data that has been acquired from selected Mass Spectrometry
detectors. Spectral data, together with chromatograms, add a third
dimension to analytical data analysis.
The MS Extension expands the capability of Clarity by providing
interactive spectral analysis, peak purity analysis and compound
identification that is based on a spectral library search. The Extension is
prepared to function with single quadrupole MS detectors and TOF MS
detectors. The Clarity is designed to acquire and evaluate data from up to
four chromatographs at a time (multi-detector measurement support). Any
Instrument within the Clarity can use the MS Extension.
All data is saved in a single file; a chromatogram at any m/z value or even
only a spectrum can simply be recalled for review after an analysis. MS
spectra, acquired using a MS detector, may be interactively selected from
a chromatogram signal for visual inspection and comparison. The spectra
may also be used for peak purity determinations and component
identification through spectral libraries. It is possible to import MS data in
AIA (cdf), mzXML, MzML and mzData formats.
The project (instrument labeled as MS - TOF ) enables to test the
capabilities of the Clarity station with the MS Extension. Several
chromatograms and one calibration are prepared for testing. This set
contains data acquired using TOF MS detector with unity precision. For
more information on the functions of the MS module, see the MS
Extension manual (downloadable at www.dataapex.com).

8.7 Demo GCxGC Project

The Clarity GCxGC (Two-dimensional gas chromatography) Extension
is a tool developed for visualizing and processing two- dimensional
chromatographic data. It is an optional Extension for the Clarity version
6.0 and newer. It expands the capability of Clarity by providing interactive
analysis and compound identification in chromatograms measured on any
gas chromatograph equipped by two columns and a modulator.

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Clarity Demo 8 Alternative demo projects
In a typical GCxGC system, the separation in the first column is based on
boiling point, while separation in the second dimension is determined by
the polarity of compounds. This will generate highly structured two-
dimensional chromatograms.
The project on the Instrument labeled My GCxGC enables to test the
capabilities of the Clarity station with the GCxGC Extension. Several
chromatograms and one calibration are prepared for testing. For more
information on the functions of the GCxGC module, see the GCxGC
Extension manual (downloadable at www.dataapex.com).

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