ChromQuest 4.

1 Quick Reference Guide

How to Use This Guide Main Menu Window
This guide contains an overview of the most common tasks that you perform in
ChromQuest. For more detailed information, refer to the ChromQuest
Chromatography Workstation User’s Guide, which contains a Tutorial, or the Online Help
online Help.
Condensed instructions are included for the following key tasks:
Task Page
• Administrating Your Enterprise 1
• Creating a Method 3
• Preparing Your Instrument for a Run 3
• Starting a Single Run 4
• Adding a Custom Report to Your Method 4
• Adding Integration Events Graphically 4
• Adding a Peak Table for Identification and Quantitation 5
• Creating a Sequence Table Using the Sequence Wizard 5
• Editing a Sequence Table 6
• Starting a Sequence Run 6
• Reprocessing a Sequence 6

If you are new to ChromQuest:

1. Launch ChromQuest. Refer to the instructions in the right column of this page.
To Launch ChromQuest:
2. Open the Instrument window. Refer to the instructions in the right column of From the desktop, choose Start > Programs > Chromatography >
this page. ChromQuest.
3. Familiarize yourself with the Instrument window. Refer to page 2.
Alternatively, double-click on the ChromQuest application icon .
4. Create a method that contains your instrument control parameters. Then, prepare ChromQuest launches and opens the Main Menu window, which is where you
your instrument for a run. Refer to page 3. perform Instrument administration and System Administration functions.
5. Inject your first sample. Refer to page 4.
To open the Instrument window:
6. After you acquire a preliminary run:
1. From the Main Menu window, double-click on the icon for your instrument
• Add a custom report to your method to produce a hardcopy of the results for
each data file. Refer to page 4. . Alternatively, right-click on the icon for your instrument. Then, choose
• Optimize the integration of your chromatogram(s). Refer to page 4. Open or Open Offline from the shortcut menu.
• Add a Peak Table to your method for the identification and quantitation 2. Log in. (If enabled)
of your analytes. Refer to page 5.
7. Create a sequence table that contains rows for your calibration standards and
samples. Then, run the sequence to enter the peak responses for your analytes See page 2
into the calibration table of the method and to quantitate your unknowns. Refer to
pages 5 and 6.

ADMINISTRATING YOUR ENTERPRISE

ChromQuest users can be given instrument administration and/or system administration privileges. Instrument administration allows you to add and configure instruments. System
administration allows you to manage users and projects. To use the project management feature, you must enable logins and create at least one user. However, after you enable
logins, only users with system administration privileges will be able to open the System Administration wizard and only users with instrument administration privileges will be
able to add or configure instruments.
To enable System Administration: To add users: ChromQuest opens the System Administration Wizard
to the Select Administration Wizard page in which you
Click on the System Administration Mode button 1. Enable System Administration.
can select the User Wizard, the Instrument Wizard, or
2. From the Main Menu menu bar, choose Tools > the Project Wizard.
to login and enable the System Administration Options to display the Options dialog box.
mode. • The User Wizard allows you to assign users access
3. Click on the Enterprise tab to display the
Enterprise page. to specific instruments and projects, as well as to
To enable logins and project limit their privileges within a project.
management: 4. Click on Add User to display the User
• The Instrument Wizard allows you to limit the
Information dialog box.
1. Enable System Administration. access of an instrument to specific users.
5. In the User Information dialog box, enter the
2. From the Main Menu menu bar, choose • The Project Wizard allows you to automate the
Tools > Options to display the Options appropriate information. Then, click on Save to organization of your data files, methods, sequences,
dialog box. close the dialog box and to add the user to the list and templates into project folders.
of Data System Users.
3. Click on the Enterprise tab to display the
Enterprise page. To open the System Administration Revision A CHROM-97102
4. Select the Enable Instrument Login and Project Wizard: Copyright© 2003 Thermo Electron.
Management checkbox. 1. Enable System Administration. All rights reserved.
Printed in the United States of America.
2. In the Main Menu toolbar, click on the
System Administration Wizard button.

1
 FAMILIARIZING YOURSELF WITH THE INSTRUMENT WINDOW
In the Instrument window, familiarize yourself with the drop-down menus in the Menu bar, the buttons in the Command toolbar, the buttons in the Integration Events toolbar,
and the shortcut menus that are accessed by right-clicking in a window.
√ Tip If you cycle the power to the Surveyor AS, wait until the autosampler completes its initialization process before you open the Instrument window.

Channel Selector Features of the Instrument Window Title Bar

Lists the discrete and multi-chromatogram Lists the instrument name, the method, the data
wavelengths that are contained in the instrument file, the pretreatment method, and the project.
setup section of the method, as well as the scan
wavelength that is currently selected, and the
spectrum max plot.
Command Toolbar
Menu Bar Contains shortcuts to the
frequently used features
of ChromQuest.

Drop-down Chromatogram
Method Menu Window Shortcut
Menu

Status Bar
Integration Events Displays the status of the
Toolbar Running Sample
run, as well as instructions
Contains the Integration Events associated with the
buttons. integration buttons.

Command Toolbar Buttons

Instrument Setup Sequence Edit Single Analysis / Display Run Queue

Displays the Instrument Setup window in Displays the Sequence table. Calibration Displays the status of the sequences and
which you enter the instrument control Allows you to apply new sample amounts single runs that have been submitted.
parameters, select auxiliary traces, enter Sequence Process to your unknowns and enter individual
the baseline check parameters, and select Displays the Sequence Process calibration levels into the peak table. Stop Run
a type of trigger. dialog box. Allows you to abort the current run, the
Preview current sequence, or all items in the
Peak / Group Tables Review Peak Calibration Allows you to preview the baseline. run queue.
Displays the Peak and Group tables for Displays the Calibration window.
the detector that is currently shown in the Single Run Main Menu
Channel Selector list box. Edit Custom Report Displays the Single Run Acquisition Displays the Main Menu window in
Displays the custom report for the active dialog box. which you perform administrative tasks.
Integration Events method.
Displays the Integration Events table for Sequence Run Instrument Wizard
the wavelength shown in the Channel Analyze Displays the Sequence Run Acquisition Displays the Instrument Wizard, which
Selector list box and the method shown in Integrates the current data file. dialog box. guides you through the creation of
the Title Bar. methods, sequences, and sample runs.

The Method Menu

Instrument Setup Window Spectral Options Window Advanced Window discrete and multi-chromatogram
wavelengths in your method.
Allows you to do the following: Contains the following pages: Library, Contains the following pages: Export,
• Enter the control parameters for each Purity, Spectrum, Multi-chromatogram, Custom Parameters, Column / Properties Dialog Box
of the modules in your instrument. and Ratio. Performance, Files, and Advanced Contains the following pages:
Reports. Description, Options, Calibration, and
• Add an auxiliary trace to record the Peaks / Groups Window
backpressure of your system during a To calculate performance parameters Audit trail.
Contains the Peak table, which is used to
run. such as capacity factor and resolution, In the Calibration page, you can do the
identify and to quantitate peaks, and the
enter your column parameters in the following:
• Enter baseline check parameters if Group tables, which are used to combine
Column / Performance page.
the Baseline Check option in the peaks into groups and to calculate group • Select the Amount / Area or the
totals. Custom Report Window Area / Amount response factor
Configuration Options dialog box is
selected. Allows you to create a report for each definition.
Review Calibration Window
data file. • Select or deselect the automatic
• Select a type of trigger. Displays the calibration table, a
graphical display of the calibration System Suitability Window averaging of standard replicates.
Integration Events Window
points, the calibration parameters, and Allows you to enter system suitability • Specify the number of standard
Contains the integration table(s) for your
the regression statistics for each parameters for each named peak and to replicates in the rolling average.
method.
named peak. perform noise and drift tests for the

2
 CREATING A METHOD
The method contains the parameters for controlling the modules of your instrument, the parameters for identifying and quantitating your chromatographic peaks, and the
parameters for determining the suitability of your system for a run. Before you can run a preliminary sample, you must create a method that contains your instrument control
parameters. After you run a preliminary sample, you can graphically optimize the integration of the resulting chromatogram(s) and to you can graphically add a Peak Table for
the identification and quantitation of your unknowns to the method.

To enter the Instrument Setup To enter the column parameters: To transfer a method:
parameters: 1. From the menu bar, choose Method > Advanced To transfer a working method from another
To develop a new chromatographic separation, begin by to display the Advanced Method Options window. chromatography data system, enter the method
entering the control parameters for the modules of your 2. Then, click on the Column / Performance tab to parameters as follows:
instrument as follows: display the Column / Performance page. 1. From the menu bar, choose File > Method >
1. From the menu bar, choose File > Method > 3. Enter the following information about your Method Wizard to display the Method Wizard.
New. column: 2. In the Method Wizard,
• Unretained Peak Time (void volume) click on the Create a Method icon .
ChromQuest opens the Instrument Setup window
with the default parameters for the configured • Column Length ChromQuest displays the Instrument Setup
modules. • Particle Diameter window, as well as an additional toolbar at the
2. In the Instrument Setup window: 4. Select the Calculate Performance Parameters for bottom of the Instrument window.
a. Enter the new instrument control parameters for This Channel checkbox. Then, select a Calculation
Method. This Channel refers to the detector. 3. Click on the Next Method Dialog button
each configured module. to move through the sections of the method.
b. In the Aux Traces page, select the pump pressure 5. Save the method.
Enter the appropriate parameters in each
trace if you want to record the backpressure of your dialog box.
system during a run. To add annotations to a trace:
c. In the Baseline Check page, enter the following: After you collect a chromatogram, add annotations that 4. After you have entered the
the length of time for which the baseline must meet will enable you to determine the performance of your contents of your method,
the test criteria, the maximum length of time for chromatographic separation. These parameters typically click on the Save Method As button
checking the baseline, and the test criteria. include capacity factor, resolution, and asymmetry. in the toolbar at the bottom of the Instrument
window.
1. Right-click in the Chromatogram window to access
the shortcut menu.
2. Click on Annotations to display the Trace
Annotation Properties dialog box. In the Available
In the example above, as soon as the baseline meets Annotations box, double-click on each annotation
the test criteria for an interval of 2 min, the run that you want to add to the trace (chromatogram).
√ Tip
begins. If the baseline does not meet the test criteria 3. Click on OK to exit the dialog box.
for 2 min within the maximum test period of 4. Save the method. If the Baseline Check option in the Configuration
10 min, ChromQuest aborts the run or the sequence. Options dialog box is enabled, include at least one
discrete channel in your scan methods.
d. In the Trigger page, select a trigger type.
Typically, the pump and detector are externally
triggered by the autosampler.
3. Save the method by choosing File > Method >
Save AS.

PREPARING YOUR INSTRUMENT FOR A RUN

Before you run a sample:
• Download the method to equilibrate your column and warm up the detector lamps.
• Check the status of the configured modules.
• Check the volume of the solvent in your Needle Wash Bottle and the volume of the
solvents in the Solvent Reservoir Bottles.
• Purge the pump if the pressure is fluctuating or if the solvent lines contain air.
• Flush the syringe if it contains air or if the tubing from the Needle Wash Bottle contains air.
• Preview the baseline.
√ Tip 1 Bar = 14.5 psi = 0.1 MPa

To download the method: To flush the Surveyor AS syringe: To purge the Surveyor LC Pump:
From the menu bar, choose Control > Download 1. Access the Direct Commands in ChromQuest as 1. Open the drain valve by turning the drain valve
Method. follows: From the Instrument Status window, click knob counter-clockwise 180° to the purge position.
on the Surveyor AS tab to display the Surveyor AS The word DRAIN on the knob will be upside
To check the Instrument Status: Instrument Status page. Then, click on down.
Diagnostics .
1. From the menu bar, choose Control >
Instrument Status. ChromQuest displays the Direct Controls page of
2. In the Instrument Status window, confirm that the the Diagnostics dialog box.
Status readout for each of the modules of your 2. From the Direct Commands list box, select Flush 2. Access the Purge group box in ChromQuest as
instrument displays Ready, with the exception of Syringe. Enter the appropriate parameters. Then, follows: From the Instrument Status window, click
the Status readout for the Surveyor LC Pump, click on Submit . on the Surveyor LC Pump tab to open the Surveyor
which displays Pump on, before you start a run. LC Pump page. Then, click on Diagnostics .
To preview the baseline: ChromQuest displays the Operation page, which
contains the Purge group box.
1. Click on the Preview button . 3. In the Purge group box, select a solvent valve and a
ChromQuest begins the baseline preview. purge time. Then, click on Purge .
2. To stop previewing the baseline, click on the 4. After you finish flushing the solvent lines, close the
drain valve by gently turning it clockwise as far as
Stop button . it will go.

3
 STARTING A SINGLE RUN
After you create a method and prepare your instrument for a run, you are ready to run a sample.

Run Information Begin Run

Sample ID. The sample ID is optional. To delay the run, click on the Clock
Data File. To add an additional icon , and then select a delay time
identifier to your data file name, click on from the list.
the blue arrow next to the data file text
box, and then make a selection from the Autosampler
popup menu. Add the .dat extension to Use Program. To perform a
the file name to distinguish its file type. Pretreatment Method, select the Use
Print Method Report. To print the Program check box. Then, click on 
method custom report at the end of the next to the text box to select a
run, select ; the Print Method Report pretreatment method.
checkbox. Vial. For the Surveyor AS, the vial
Amount Values locations for the standard vial types are
A;1 to E;40. For the AS1000 and the
Entries in this group box affect the AS3000, the vial locations for the
quantitation of unknown run types. standard vial types are A01 to C40.
Quantitated peaks are divided by the
Sample Amount value and the Dilution Injection Volume. For the Full Loop To inject a single sample: To extend the run:
Factors values, and are multiplied by the Injection mode, match the injection
Multiplication Factors values. volume to the sample loop size. For the 1. In the Command toolbar, Choose Control > Extend Run from
Partial Loop Injection mode, inject no click on the Single Run the menu bar.
Baseline Check more than half the sample loop size. For button to display the Single Run
To perform a noise and drift test before the No Waste injection mode, inject at Acquisition dialog box. To abort the run:
the autosampler injects the sample, least 0.5 µL. The maximum injection 2. Make the appropriate entries and In the Command toolbar,
select ; the Baseline Check checkbox. volume for the no waste injection mode selections. click on the Stop button.
In addition, ensure that your method is 5 µL less than the sample loop size. 3. To start the run, click on Start .
contains baseline check parameters.

ADDING A CUSTOM REPORT TO A METHOD

To print a report for each data file, you need to add a custom report to your method. You can add one of the four standard templates, or you can create your own custom
template. After you create a custom report template, you can add it to other methods as well as the current method.

To add a Custom Report to the To create a new Custom Report

method: Template:
1. In the Custom Report window, place the cursor at
1. Click on the Edit Custom Report button . the desired location.
If this is a new method, a blank page appears. 2. Right-click to display the shortcut menu.
3. Choose a menu item.
2. From the menu bar, choose
File > Report Template > Open to access one 4. After you finish creating the custom report,
of the four standard custom report templates. choose File > Report Template > Save As
from the menu bar to display the Save As
External Standard.srp dialog box.
Internal Standard.srp
5. Type in a name for the Custom Report Template.
√ Tip
Area %.srp
Normalization.srp Then click on Save . If you want the template to appear in the list that you
access by choosing Reports > View from the menu
3. Save the method. ChromQuest adds the [.rep] extension to the file.
bar, add an [.srp]. extension to the file name.

ADDING INTEGRATION EVENTS GRAPHICALLY

You can optimize the integration of your chromatogram(s) by graphically adding integration events. By default, the Integration Events table for each wavelength channel
contains an integration event for Width that is set to a value of 0.2 min and an integration event for Threshold that is set to a value of 50.

To graphically add integration To open a stored data file:

events: 6. Click on Analyze Now to add the event to the
1. Choose File > Data > Open from the menu bar.
integration table and to apply the event to the
1. Use your current data file or open a stored chromatogram. ChromQuest displays the Open Data File
data file. 7. To review the Integration tables, dialog box.
2. From the Channel Selection list box, select 2. In the Open Data File dialog box, select a directory
a wavelength. click on the Integration Events button to look in.
Each wavelength has its own Integration table(s). 3. Click on a data file from the list in the left pane.
or the Manual Integration Fixes button
3. Click on the chromatogram to activate the on the Command toolbar. You can see a preview of the chromatogram(s) in
integration toolbar. the data file by clicking on the Preview button
4. In the Integration Events toolbar, click on an
integration event button, and then follow the Note. The Integration Events tables are stored in , or you can view the file description by
instructions shown in the status bar. the method file. The Manual Integration Fixes
tables are stored in the data file. clicking on the Description button .
A dialog box appears upon completion.
5. Select the Insert into Integration Events Table 4. Click on Open to open the selected data file.
option button to apply the event to every data file
processed with this method or select the Insert into
Manual Integration Fixes Table option button to
apply the event to only the current data file.

4
 ADDING A PEAK TABLE FOR IDENTIFICATION AND QUANTITATION
The peak table contains the information required to identify the peaks in the chromatogram(s), as well as the information required to build the calibration curve(s).
The peak table also contains the concentration values of the check standards and the sample spikes. There is one peak table for each detector in your instrument.
For multi-wavelength analyses, use the Analysis Channel column in the peak table to specify the calibration wavelength(s).
Peak Table
Properties
By default, the Fit Type
is Point-to-Point and the
Calib Flag is Replace.

To create the Peak table: To change the number of calibration

1. Open a stored data file. levels: Note. The peak table
2. Click anywhere in the Chromatogram window to 1. Right-click in the Peak Tables window to display shown above contains
activate the Integration Events toolbar, and then the shortcut menu. three concentration levels.
2. Click on Properties to display the Properties
click on the Define Peaks button . dialog box.
3. Follow the instructions in the status bar. 3. In the Properties dialog box, double-click on
After you graphically select your peak range, Levels to display the Max # of levels text box.
ChromQuest displays the Define Peaks Type a new value into the text box. Then, press
dialog box. the <Enter> key.
4. Make the appropriate selections in the Define To quantitate peaks on more than
Peaks dialog box. one Analysis Channel:
√ Tip The Minimum Peak Area or Peak Height list 1. Click on the peak # to highlight the entire row.
box allows you to exclude peaks below the selected Then, copy the information to a new row.
value from the Peak table.
2. Click on the down arrow in the Analysis Channel
5. Click on OK to exit the dialog box. column. Then, select the Analysis Channel from
the list of available wavelengths.
6. Click on the Peak / Group Tables button
to review the information in the Peak table.

Before you run a set of samples…

To automatically inject a set of samples, you need to create a sequence table. To make the task easier, ChromQuest contains a Sequence Wizard.
However, the Sequence Wizard does not contain all the available sequence options. You need to edit the sequence table if you want to add
run types that are not available in the Sequence Wizard. After you run your sequence, you might want to modify the method, and then reprocess the
data. For more information, refer to the following topics:
• Creating a Sequence Table Using the Sequence Wizard
• Editing a Sequence Table
• Starting a Sequence Run
• Reprocessing a Sequence

CREATING A SEQUENCE TABLE USING THE SEQUENCE WIZARD

The Sequence table contains the information that is required to automatically inject a set of samples or to reprocess a set of stored data files. ChromQuest contains a
Sequence Wizard that guides you through the creation of a Sequence table.

To open the Sequence Wizard: To create a sequence from existing 4. Click on Open .
data files: 5. Click on Finish .
From the menu bar in the Instrument Window, choose
1. On the Method page, do the following: 6. Save the sequence.
File > Sequence > Sequence Wizard.
a. Click on  and then select a method from a
ChromQuest displays the Method page of the ChromQuest directory.
Sequence Wizard. b. Select the From Existing Data Files √ Tip
To create an acquisition Sequence: option button. Then, click on Next to In the Method page, the values entered in the Amount Values
display the Select Files page. group box affect how ChromQuest reports the concentrations
1. On the Method page, select the For Acquisition
option button. 2. Click on  to display the Open Data of the quantitated peaks in your unknowns as shown in the
Files dialog box. Then, open the following equation.
2. Make the appropriate selections and entries in the ChromQuest directory that contains your
Method, Unknowns, Autosampler, Calibration, data files. [Unk]C × Multiplier 1 × Multiplier 2 × Multiplier 3 = [Unk]R
and Reports pages of the Sequence Wizard.
3. Click on the last data file that you want to Sample Amt × Dilutor 1 × Dilutor 2 × Dilutor 3
3. After you complete your entries, click on reprocess, hold down the <Shift> key.
Finish . Then, click on the first data file that you Where
The Sequence window opens. want to reprocess. [Unk] = the concentration of the unknown determined from the
C
4. Save the Sequence table by choosing File > A list of the selected data files appears in calibration curve
Sequence > Save As from the menu bar. the pane in the order that they will appear [Unk]R = the concentration of the unknown reported by
in the sequence table. ChromQuest

5
 EDITING A SEQUENCE TABLE
The Sequence Wizard allows you to create a basic Sequence table. Typical modifications to the basic sequence table include the following:
• Adding a Shutdown run type to shut down your instrument at the end of a sequence run
• Adding a Baseline Check run type to perform a baseline check at the beginning of a sequence run
• Adding an Action, such as running a shutdown if a hardware status error occurs
• Changing the Sequence Summary Template if you do not want to use the default template

To edit the sequence: To add a shutdown run type: To change the sequence summary
1. In the last row of the sequence table, double-click template:
Click on the Edit Sequence button to open your in the Run Type column to display the Sample Run
sequence table. The default template (Summary.tpl) reports the
Types dialog box.
concentrations of your named peaks for the first
You can change the run type of any row in the table. 2. Select the Shutdown run type. wavelength in the Channel Selection list box.
The run type options are as follows: 3. In the Method column, click on the green arrow,
and then select a shutdown method. You can access other sequence summary reports from
the template directory as follows:
4. Save the sequence.
To minimize scrolling, you 1. Double-click in the Run Type cell that contains the
can deselect the properties To add a baseline check run type: Begin Summary (SMB) run type.
that you do not need from
the table. The sequence 1. Enter the appropriate baseline check parameters in 2. Click on the Begin Summary check box to display
can contain the following the Instrument Setup section of the method. the contents of the Report Template text box.
properties: 2. In the first row of the sequence table, double-click 3. Click on  to select a summary report template
in the Run Type column to display the Sample Run from the following list of templates.
Types dialog box. Vial Summary.tpl
3. Select the Baseline Check run type. Trend.tpl
4. Save the sequence. Summary.tpl
4. Save the sequence.
To add an Action:
√ Tip
1. If you want to perform an action for a run, click on
To create your own sequence summary template:
the blue arrow in the Action column to display the
Action dialog box. Choose File > Advanced Reports > New from the
2. Select the tests that you want to perform. Command menu bar. ChromQuest displays the
3. For each test, select whether ChromQuest performs Template Editor window. Click on a cell in the
spreadsheet. Then, click on either the Table Wizard
the action if the test passes or if the test fails. Then,
select the resulting action. Some actions will button or the Function Wizard button.
require additional parameters.

STARTING A SEQUENCE RUN REPROCESSING A SEQUENCE

To start a sequence run: To reprocess a sequence:

1. Click on the Sequence Run button to open the Sequence Run dialog box. 1. Click on the Process a Sequence button .
2. Click on  to select a sequence file from a ChromQuest directory. 2. Click on  to select a sequence file from a ChromQuest directory.
3. Select the All or the Range option button for the Run range. 3. Select the All or the Range option button.
Enter a contiguous range with a dash (1-10). Enter a non-contiguous range with 4. Select a processing mode from the Processing Mode list box.
a comma (1-10,20-30). Use Stored Results shows the original results.
Use Last Results shows the most recent results.
If you selected a section of the sequence before you opened the Sequence Run Reintegrate recalculates the results.
dialog box, notice that ChromQuest has automatically selected the ~ Selection Review Only displays the results on the screen.
option button.
5. Select a type of bracketing from the Bracketing list box.
4. Select a processing mode from the Processing Mode list box.
6. Select the Review Results check box to pause the processing after each data file.
For HPLC systems, select Normal. For systems that contain an HS2000 or an Click on the green up and down arrows× ×Ø
× Ø
Øto move through the rows of the
HS850, select Full Download. sequence.
5. Select a type of bracketing from the 7. To print the custom report for each data file,
Bracketing list box. select ; the Print Method Reports checkbox.
6. To print the custom report for each data file, To print the sequence reports,
select ; the Print Method Reports checkbox. select ; the Print Sequence Reports
To print the sequence reports, checkbox.
such as the Sequence Summary report 8. Click on Start .
and the System Suitability report, 9. Click on the
select ; the Print Sequence Reports Review Peaks Calibration button
checkbox. to review the calibration curve.
7. Click on Start .