ChromQuest 5.

0 Quick Reference Guide

This guide contains an overview of the ChromQuest™
chromatography data system, with topics organized by workflow. For Adding and Configuring Instruments
more information, refer to the ChromQuest 5.0 User Guide, the
Y To add an instrument to the Enterprise
manuals for the liquid or gas chromatography instruments, and the
Help provided with ChromQuest. The manuals are provided as Right-click The Enterprise and choose New Instrument.
PDFs on the ChromQuest installation CD. Y To configure an instrument
1. Do one of the following:
Contents • In ChromQuest, right-click the instrument icon and choose
• Starting ChromQuest Configure > Instrument.
• Adding and Configuring Instruments • In ChromQuest SI, choose Start > All Programs >
• Administrating ChromQuest Chromatography > ChromQuest SI Config. In the
• Opening the Instrument Window ChromQuest SI Configuration dialog box, click Instrument
• Creating a Method Configuration.
• Adding Column Specifications to a Method The Instrument Configuration dialog box appears.
• Preparing the Instrument for a Run
• Starting a Single Run
• Adding Annotations to a Chromatogram
• Adding a Custom Report to a Method
• Adding Integration Events Graphically
• Identifying and Quantitating Analytes
• Creating a Sequence
• Editing a Sequence Table
• Starting a Sequence Run
• Reprocessing a Sequence 2. In the Instrument name box, type a name for the instrument.
3. Do one of the following:
• To configure a new instrument, in the Instrument type list,
Starting ChromQuest select the instrument type.
• To modify the configuration of an existing instrument, go to
Y To start ChromQuest or ChromQuest SI
step 4. (Do not make a selection in the Instrument type list,
From the computer desktop, choose Start > All Programs > as doing so erases the current instrument configuration.)
Chromatography > ChromQuest or ChromQuest SI.
4. Click Configure. The instrument dialog box appears.
For ChromQuest, the Main Menu window appears. Use this 5. In the Available modules list, double-click the icons for the
window to configure instruments and administrate ChromQuest. instrument modules. The icons appear in the Configured
Login icon Help icon modules list.
6. For PDA detectors, do the following:
a. In the Available modules list, double-click the Detector icon.
The Analog icon appears in the Configured modules list.
b. Double-click the Analog icon. The Detector Configuration
dialog box appears.
c. In the Detector model list, select PDA or PDA Plus.
d. Click . Do not change the Stack number unless you are
controlling more than one PDA from the same computer.
The Stack number must match the rotary switch setting on
the back panel of the instrument.
e. Click OK to close the PDA Plus dialog box. Click OK to
close the Detector Configuration dialog box.
7. To complete the configuration of each device, refer to the Help
provided with ChromQuest.
8. To save the configuration settings and close the instrument dialog
box, click OK.
For ChromQuest SI, the Instrument window appears (see page 2).

Revision A CHROM-97254
Copyright© 2008 Thermo Fisher Scientific Inc.
All rights reserved.
 Icon Tooltip Use
Administrating ChromQuest Integration Events Opens the Integration Events table for the
current method and the wavelength
You can limit access to specific tasks by assigning instrument and displayed in the Channel Selector list.
system administration privileges. Users with instrument
Manual Integration Opens the Integration Events table for the
administration privileges can add and configure instruments. Users Fixes current data file and the wavelength
with system administration privileges can manage users and projects. displayed in the Channel Selector list.
Y To enable logins and project management Sequence Edit Opens the Sequence window.
1. In the Main Menu toolbar, click to log in and enable the
Sequence Process Opens the Sequence Process dialog box.
System Administration mode.
2. In the menu bar, choose Tools > Options. Review Peak Opens the Review Peak Calibration
3. In the Options dialog box, click the Enterprise tab. Calibration window.
4. On the Enterprise page, select the Enable Instrument Login Edit Custom Report Opens the custom report for the active
and Project Management check box. method.
5. Click Add User. The User Information dialog box appears. Analyze Integrates the current data file.
6. Enter the appropriate information, and then click Save. The user
name appears in the Data system users list. Single Analysis/ Applies sample amounts to the unknowns
7. In the toolbar, click . The System Administration Wizard Calibration and enters calibration levels into the peak
appears. table.
8. Use these wizards to create projects and assign privileges: Preview Starts a preview of the baseline.
• To assign users access to instruments and projects and
privileges within a project, select the User Wizard. Single Run Opens the Single Run Acquisition
• To assign access to instruments, select the Instrument dialog box.
Wizard. Sequence Run Opens the Sequence Run Acquisition
• To create project folders for data files, methods, sequences, dialog box.
and templates, select the Project Wizard. Display Run Queue Displays the status of the submitted
sequences and single runs.
Opening the Instrument Window Stop Run Stops the current run, the current
sequence, or all items in the run queue.
Y To open the Instrument window in ChromQuest Instrument Wizard Guides you through the creation of
methods, sequences, and sample runs.
1. In the Main Menu window, right-click the icon for your
instrument and choose Open or Open Offline.
Title Bar displays the instrument name, method,
2. Log in and select a project in the Project list, if enabled.
data file, pretreatment method, and project.
The project folder becomes the default location for data files,
methods, sequences, and template files. Channel Selector list contains the discrete and
multi-chromatogram wavelengths specified in
the method, selected scan wavelength, and
spectrum max plot.

Command Toolbar Menu Bar

The Instrument window appears.

Y To open the Instrument window in ChromQuest SI
From the computer desktop, choose Start > All Programs >
Chromatography > ChromQuest SI.
Familiarize yourself with the menus, Command toolbar icons,
Integration Events toolbar icons, and shortcut menus accessed by
right-clicking the window.
Icon Tooltip Use
Instrument Setup Opens the Instrument Setup window
where you specify the instrument Integration Events toolbar
parameters, auxiliary traces, baseline contains the Integration
check parameters, and trigger type. Events icons. Status Bar displays the run
Peak/Group Tables Opens the Peak and Group tables for the status, as well as
detector currently shown in the Channel instructions associated
Selector list. with the integration icons.

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 for each detector. System suitability results are wavelength
Creating a Method dependent. You can add peak parameter annotations, such as
resolution, capacity factor, and asymmetry, to chromatograms
The method contains instrument control, peak identification, without adding a peak table to the method.
calibration, and system suitability parameters. To acquire data, the 6. Save the method.
method must include the chromatographic conditions, such as the
mobile phase composition, flow rate, analysis wavelengths, and Preparing the Instrument for a Run
injection type, as well as the trigger type.
For best results, make sure that your chromatographic system is ready
Y To develop a new chromatographic method
before running samples.
To add the chromatographic conditions for your application to the
method, use the New Method template. Y To download the method
1. In the Instrument window, choose File > Method > New. The From the menu bar, choose Control > Download Method.
Instrument Setup window appears with the default parameters
Y To check the instrument status
for the configured modules.
2. Specify the control parameters for each configured module. 1. From the menu bar, choose Control > Instrument Status.
3. (Optional) On the Aux Traces page, select the pump pressure 2. In the Instrument Status window, before you start a run, confirm
trace to record the backpressure of the LC system during a run. that the Status readout for each module displays Ready, with the
4. On the Trigger page, select a trigger type (typically External— exception of the Status readout for the Surveyor LC Pump Plus,
the autosampler triggers the start of data acquisition). which displays Pump on.
5. Choose File > Method > Save As to save the method. Y To preview the baseline
Y To transfer an existing method created with another data system 1. Choose Control > Preview Run. The baseline preview starts.
1. From the menu bar, choose File > Method > Method Wizard to 2. To stop the baseline preview, click (Stop Run).
display the Method Wizard. Y To perform a baseline check
2. In the Method Wizard, click (Create a Method). The 1. Choose Control > Baseline Check.
Instrument Setup window appears with an additional toolbar 2. On the Baseline Check page, enter the following:
( ) at the bottom of the window. • The length of time the baseline must meet the test criteria
3. Click to move through the sections of the method. Enter the • The maximum length of time for checking the baseline
appropriate parameters in each dialog box. • The test criteria
4. After you enter the contents of your method, click (Save
Method As) at the bottom of the window. In the following example, when baseline meets the test criteria for an
interval of 2 minutes, the run begins. If the baseline does not meet
Y To create a shutdown method for a Surveyor or SpectraSYSTEM LC the criteria within the 10 minute test period, the run stops.
1. Open the Instrument Setup window.
2. On the detector page, clear the lamp check boxes and select the
Shutdown method check box.
3. On the pump page, set the flow rate to zero and select the
Shutdown method check box.
4. Save the method and use it at the end of a sequence to turn off
the detector lamps and mobile phase flow.
Tip The Accela Pump does not support shutdown methods.
To turn off the mobile phase flow at the end of a sequence run, Tip For scans, include at least one multi-chromatogram channel
select the Stop after the end in the Method Finalizing list. in the method.

Adding Column Specifications to a Method Starting a Single Run

To calculate the suitability of a chromatographic run, add After you create a method and prepare your instrument for a run,
information about the chromatographic column to the method. you are ready to inject a sample.
Y To specify the column parameters Y To inject a single sample
1. From the Instrument window, open the method. 1. Load the sample into the autosampler.
2. Choose Method > Advanced.
2. In the Command toolbar, click (Single Run).
3. In the Advanced Method Options window, click the Column /
3. In the Single Run Acquisition dialog box, make the appropriate
Performance tab. The Column/Performance page appears.
entries and selections. See the parameters table on page 4.
4. For the column, specify its unretained peak time (void volume),
length, and particle diameter. 4. To delay the start of the run, click and select a time in
5. Select the Calculate Performance Parameters for This Channel the list.
check box, and then select a calculation method. Channel is the 5. To start the run, click Start.
detector, not the analysis wavelength. For a multiple detector 6. To extend the run, choose Control > Extend Run.
system, you can specify different column performance parameters 7. To stop the run, click (Stop Run).

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Run information area Calibrate area Adding Annotations to a Chromatogram
Annotations include information about the chromatographic peaks
such as the peak names and retention times. ChromQuest adds the
peak name annotation after you create a peak table with the peak
names and expected retention times.
Y To add annotations to a trace
1. Right-click the Chromatogram window.
2. In the shortcut menu, choose Annotations. The Trace
Annotation Properties dialog box appears.
3. In the Available Annotations list, double-click each annotation
that you want to add to the trace (chromatogram).
4. Click OK to close the dialog box.
5. Save the method.

Amount values Autosampler Begin run Baseline Check Adding a Custom Report to a Method
area area area check box
To print a report for each data file, add a custom report to the
Parameter Description method. You can select one of the four standard templates, or you
can create your own custom template.
Run information area
Sample ID (Optional) Y To add a custom report to the method
Method Contains the information required to acquire and process 1. Choose Method > Custom Report. If this is a new method, a
data files. blank page appears.
Data path Location where ChromQuest stores the data files. 2. From the menu bar, choose File > Report Template > Open.
Data file The name of the data file. Clicking the blue arrow opens a 3. Select one of the four standard custom report templates:
list of unique identifiers, such as increment number. • External Standard.srp
Number of reps Specifies the number of times the current sample is to be • Internal Standard.srp
injected. To make one injection, use the default value of 1. • Area%.srp
Print method Select this check box to print the custom report. • Normalization.srp
report
4. Save the method.
Amount values area
For most runs, use the default values of 1. If the method contains a calibration
Y To create a new custom report template
curve, enter multiplication factors and dilution factors to calculate the original 1. In the Custom Report window, place the cursor where you want
sample concentration or amount. the item to appear.
[Unk] C × mult factor 1 × mult factor 2 × mult factor 3 2. Right-click and choose an item in the shortcut menu.
--------------------------------------------------------------------------------------------------------------------------------- = [ Unk ] R
sample amount × dilution 1 × dilution 2 × dilution 3 3. After you finish adding items, choose File > Report Template >
[Unk]c = the concn of the unknown determined from the calibration curve Save As. The Save As dialog box appears.
[Unk]R = the concn of the unknown reported by ChromQuest 4. Type a name for the Custom Report template and click Save.
Autosampler area
ChromQuest adds the .rep extension to the file. To make the
Use program Clear the Use program check box unless you want the
template appear in the Reports list, replace .rep with .srp.
autosampler to perform a pretreatment method before it Data graph
makes an injection.
Vial Specifies the vial or well where the autosampler withdraws
the sample. For the Surveyor or Accela Autosamplers, the
allowable values are A;1 to E;40 (for vials), A;A1 to C;H12
(for 96-well plates), and A;A1 to C;P24 (for 384-well plates).
For the AS3000, the allowable values are A1 to E40.
Injection volume For partial loop and no waste injections, this is the volume
that the autosampler meters into the sample loop. With
ChromQuest, you cannot inject volumes greater than the
configured sample loop size. The method specifies the
injection type.
Calibrate area
Use this option to inject the calibration standards one at a time.
Baseline check option
Use this option to delay an injection until the baseline stabilizes.
Begin run area
Use this feature to delay the start of the run. Run report

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 Y To create the peak table
Adding Integration Events Graphically 1. Open a stored data file.
2. In the Integration Events toolbar, click (Define Peaks).
You can optimize the integration of your chromatograms by
3. Follow the instructions in the status bar. After you graphically
graphically adding integration events. By default the
select the peak range, the Define Peaks dialog box appears.
Integration Events table for each wavelength channel contains the
4. Make the appropriate selections. Use the Minimum Peak Area or
Width integration event set to a value of 0.2 minutes and the
Peak Height list to exclude peaks below the selected value from
Threshold integration event set to a value of 50.
. the Peak table.
5. Click OK to close the dialog box.
6. Choose Method > Peaks/Groups to review the information in
the peak table.
Y To change the number of calibration levels
Y To add integration events graphically 1. Right-click the Peak Tables window and choose Properties.
1. Use your current data file or open a stored data file. 2. In the Properties dialog box, double-click Levels to display the
2. In the Channel Selector list, select a wavelength. Each wavelength Max # of levels box.
has its own Integration Events and Manual Integration Fixes 3. Type a new value in the box, and then press the ENTER key.
tables.
Y To quantitate peaks on more than one Analysis Channel
3. Click the chromatogram to activate the integration toolbar.
4. In the Integration Events toolbar, click an integration event icon, 1. To highlight the entire row for a peak, select the # column, and
and then follow the instructions shown in the status bar. A dialog then copy the information to a new row.
box appears upon completion. 2. Click the down arrow in the Analysis Channel column and select
5. To apply the event to every data file processed with this method, the wavelength of interest in the list of available wavelengths.
select the Insert into Integration Events Table option. Or to
apply the event to only the current data file, select the Insert into Creating a Sequence
Manual Integration Fixes Table option. A sequence table contains the information required to automatically
6. To add the event to the integration table and to apply the event inject a set of samples or to reprocess a set of stored data files. The
to the chromatogram, click Analyze Now. Sequence Wizard helps you create a basic sequence table.
7. Review the Integration tables:
Y To open the Sequence Wizard
• To open the Integration Events table, click .
• To open the Manual Integration Fixes table, click . In the Instrument window, choose File > Sequence > Sequence
Wizard.
The Integration Events tables are stored in the method file. The
Manual Integration Fixes tables are stored in the data file. Y To create an acquisition sequence
Y To open a stored data file 1. On the Method page, select the For Acquisition option.
2. Make the appropriate selections and entries on the Method,
1. In the Instrument window, choose File > Data > Open. The
Unknowns, Autosampler, Calibration, and Reports pages of the
Open Data File dialog box appears.
Sequence Wizard.
2. Browse to the appropriate directory.
3. After you complete your entries, click Finish. The Sequence
3. Select a data file.
window appears with the sequence table.
4. (Optional) To see a preview of the chromatograms in the data
file, click . To view the file description, click .
5. Click Open. The Chromatogram view for the wavelength
displayed in the Channel Selector list appears. When the data file
contains spectral data, the Mixed View appears.
4. Choose File > Sequence > Save As to save the sequence.
Identifying and Quantitating Analytes
Y To create a sequence from existing data files
The peak table contains the information required to identify the
1. On the Method page, do the following:
chromatographic peaks and build the calibration curves for the
analytes. It also contains the concentrations of the check standards a. Click and select a method.
and sample spikes. There is one peak table for each detector of your b. Select the From Existing Data Files option, and then click
instrument. For multi-wavelength analyses, use the Analysis Channel Next to display the Select Files page.
column in the peak table to specify the calibration wavelengths. 2. Click to display the Open Data Files dialog box, and then
Three concentration levels browse to the folder that contains the data files.
Two analysis wavelengths 3. To create an ordered list of data files, select a data file and click
Add for each data file that you want to reprocess. The data files
appear in the Data File list at the bottom of the dialog box.
4. Click Open. The Select Files page appears.
5. Check the list of data files and click Finish.
6. Save the sequence.

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 Editing a Sequence Table Starting a Sequence Run
Use the Sequence Wizard to create a basic sequence table. Edit the Y To start a sequence run
sequence table to do the following: 1. Choose Control > Sequence Run to open the Sequence Run
• Add a Baseline Check run type to the first row of the sequence. dialog box.
• Add a Shutdown run type to the last row of the sequence.
2. Click to browse for and select a sequence file.
• Add an Action, such as running a shutdown if a hardware status
3. For the Run range, select the All or the Range option. For a
error occurs.
contiguous range, use a dash, as in 1-10. For a non-contiguous
• Change the Sequence Summary template.
range, use a comma, as in 1-10,20-30.
Y To edit the sequence 4. In the Mode area, in the Processing mode list, select Normal. In
Choose Sequence > Edit. The sequence table appears. You can the Bracketing list, select a type of bracketing.
modify the sample run types for any row in the table. 5. In the Printing area, to print the custom report for each data file,
select the Print method reports check box. To print the
Y To modify the run type selections
sequence reports, such as the Sequence Summary report and the
1. Double-click the Run Type column in the appropriate row of the System Suitability report, select the Print sequence reports
sequence. The Sample Run Types dialog box appears. check box.
6. Click Start.

Reprocessing a Sequence
2. Select the check box for the run type of interest. You can select Y To reprocess a sequence
multiple run types for each sequence row. Make additional 1. Choose Sequence > Process.
selections as necessary: 2. In the Sequence Process dialog box, click to browse for and
• To add a baseline check run type, double-click the Run Type select a sequence file.
column in the first row of the sequence table and select the 3. Select the All or the Range option.
Baseline Check check box. 4. In the Processing mode list, select a processing mode:
• To add a shutdown run type, double-click the Run Type • Use Stored Results shows the original results.
column in the last row of the sequence table and select the • Use Last Results shows the most recent results.
Shutdown check box. In the Method column, select a • Reintegrate recalculates the results.
shutdown method. • Review Only displays the results in the Instrument window.
• To change the sequence summary template, double-click 5. In the Bracketing list, select a type of bracketing.
the Run Type cell that contains the Begin Summary (SMB) 6. To pause the processing after each data file, select the Review
run type. Select the Begin Summary check box to check box and the Results review option. To move through the
display the contents of the Report Template box. Click sequence rows, click the blue up and down arrows,
to browse for and select a summary report template. (Previous) and (Next).
3. Save the sequence. 7. To print the custom report for each data file, select the
The default template (Summary.tpl) reports the concentrations of the Print method reports check box. To print the sequence reports,
named peaks for the first wavelength in the Channel Selector list. select the Print sequence reports check box.
8. Click Start.
9. To review the
calibration curve,
click .

For information on creating a custom summary report template,

refer to the ChromQuest Help. Accela, ChromQuest, and Surveyor are trademarks of Thermo Fisher Scientific, Inc.