Manual Workstation

NOTICE: Varian, Inc.
was acquired by Agilent

Technologies in May 2010. This document is provided
as a courtesy but is no longer kept current and thus
will contain historical references to Varian. For more Varian, Inc.
information, go to www.agilent.com/chem. 2700 Mitchell Drive
Walnut Creek, CA 94598-1675/USA
MS Workstation
Tutorial Manual
©Varian, Inc. 2003-2006 Printed in U.S.A. 03-914988-00:Rev. 3

Contents
Exercises...................................................................................................................................7
Overview.....................................................................................................................................................................7
Executing Exercises ...................................................................................................................................................7
Running an MS Method without a GC Method ....................................................................................................8
Loading an MS File in MS Data Review ..............................................................................................................9
Displaying Mass Chromatograms ......................................................................................................................11
Getting Spectra from an MS file .........................................................................................................................15
Performing a Background Correction.................................................................................................................16
Performing a NIST Library Search.....................................................................................................................19
How to Create or Edit NIST libraries..................................................................................................................21
Building a Spectrum List ....................................................................................................................................22
Editing Spectra...................................................................................................................................................25
Printing Pictures ................................................................................................................................................26
Exporting Pictures ..............................................................................................................................................27
Creating and Using a Spooler File .....................................................................................................................28
Exporting Spectra...............................................................................................................................................31
Displaying and Printing Log Information ............................................................................................................32
Acquiring a 2000 MS Data File...............................................................................................35

Introduction ...............................................................................................................................................................35
Starting the Varian MS Workstation .........................................................................................................................35
Setting Instrument Configuration for Manual Injections............................................................................................35
Running an MS Method without a GC Method ..................................................................................................37
Adjusting and Tuning the 2000.................................................................................................................................38
Adjusting RF Tuning...........................................................................................................................................40
Adjusting Calibration Gas...................................................................................................................................40
Adjusting CI Reagent .........................................................................................................................................41
Running Auto Tune ............................................................................................................................................42
Examining Current Module Attributes ................................................................................................................43
Preparing a GC/MS Acquisition Method...................................................................................................................44
Creating a New Method .....................................................................................................................................44
Editing the Method .............................................................................................................................................48
Starting the Acquisition.............................................................................................................................................53
Activating the GC/MS Method............................................................................................................................53
Starting the GC/MS Run ....................................................................................................................................54
Injecting 1 µL of the Column Test Mixture .........................................................................................................56
Monitoring Data Acquisition in Progress from System Control ..........................................................................57
Monitoring the Acquisition in Progress from MS Data Review ..........................................................................59
Retention Times for Analytes in the Column Test Mix Sample..........................................................................61
Setting Instrument Configuration for Automated Injections ......................................................................................61
Configuring the Instrument.................................................................................................................................61
Creating the Sample List....................................................................................................................................66
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Qualitative Analysis of GC/MS Data......................................................................................69
Analyzing GC/MS Data.............................................................................................................................................69
Demonstration Files ...........................................................................................................................................69
Displaying a Data File ........................................................................................................................................70
Choosing a Mass Spectrum ...............................................................................................................................71
Background Correction ......................................................................................................................................71
Running a Library Search on a Single Spectrum...............................................................................................72
Creating a Spectrum List....................................................................................................................................74
Library Searching a Spectrum List.....................................................................................................................75
Performing a Chromatogram Search with a Spectrum List ...............................................................................76
Quantitative Analysis of GC/MS Data ...................................................................................79

Overview of the Quantitative Analysis Tutorials .......................................................................................................79
Demonstration Files ...........................................................................................................................................79
Tutorial Topics....................................................................................................................................................80
Qualitative Identification ...........................................................................................................................................81
Editing a Data Handling Method...............................................................................................................................81
The Calculations Setup Dialog Box ...................................................................................................................84
The Results Treatment Dialog Box ....................................................................................................................87
The Compound Table ........................................................................................................................................87
Building a Recalculation List for Calibration ...........................................................................................................104
Processing a Recalculation List to Add Calibration Data .......................................................................................108
Examining Calibration Results in Process Data View......................................................................................108
Reviewing Calibration Results in the Results View ................................................................................................110
Viewing and Editing Calibration Results in the Method Builder Dialog............................................................115
Processing Analysis Files in a RecalcList ..............................................................................................................117
Adding and Processing Entries in an Existing RecalcList................................................................................118
Reviewing Analysis Results....................................................................................................................................124
SIS and MS/MS Acquisitions ...............................................................................................127

Introduction Tutorial ................................................................................................................................................127
Calibration of SIS .............................................................................................................................................127
MS/MS..............................................................................................................................................................130
Run File Tutorials .................................................................................................................145

Overview of the Varian MS Workstation for GC Run Files.....................................................................................145
Using the Star Toolbar............................................................................................................................................145
Using the Tutorials..................................................................................................................................................146
Example Files...................................................................................................................................................146
Reinstalling the Tutorial Files ...........................................................................................................................146
Tutorial 1 Recalculating Results ........................................................................................147

Overview.................................................................................................................................................................147
Preparing a Data File for Use with this Tutorial......................................................................................................147
Opening a Data File and Method in Interactive Graphics.......................................................................................147
Moving a Peak Event..............................................................................................................................................152
Recalculating the Data File.....................................................................................................................................153
Editing the Method..................................................................................................................................................155
Recalculating in System Control.............................................................................................................................157
Tutorial 2 Changing Peak Detection Parameters..............................................................161

Overview.................................................................................................................................................................161
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Preparing the Data File for Use with this Tutorial...................................................................................................161
Opening the Data File and Method.........................................................................................................................161
Changing the Initial Peak Width .............................................................................................................................163
Changing the Signal-to-Noise Ratio .......................................................................................................................167
Changing the II Time Events ..................................................................................................................................168
Changing the WI Time Event..................................................................................................................................171
Tutorial 3 Filling a Peak Table ............................................................................................173

Overview.................................................................................................................................................................173
Opening the Fill Peak Table Window .....................................................................................................................173
Adding Peaks with the cursor .................................................................................................................................174
Adding Peaks from a selection ...............................................................................................................................174
Naming Peaks ........................................................................................................................................................175
Designating Peak Functions...................................................................................................................................176
Reference Peak(s) ...........................................................................................................................................176
Internal Standard Peak(s) ................................................................................................................................176
Relative Retention Time Peak .........................................................................................................................176
Entering Amounts for Calibration Levels ................................................................................................................177
Editing the Peak Table ...........................................................................................................................................177
Tutorial 4 Identifying Peaks ................................................................................................179

Overview.................................................................................................................................................................179
Peak Windows ........................................................................................................................................................179
Define Peak Windows.............................................................................................................................................180
Showing Peak Windows .........................................................................................................................................181
Changing Peak Functions ......................................................................................................................................182
Peak Reject ............................................................................................................................................................183
Unidentified Peaks..................................................................................................................................................184
Tutorial 5 Using the II, SR, and VB Time Events ...............................................................185

Overview.................................................................................................................................................................185
Inhibiting Integration ...............................................................................................................................................185
Editing a Time Event from the Menu ......................................................................................................................187
Graphical Placement of a Time Event ....................................................................................................................189
Using Solvent Reject ..............................................................................................................................................191
Using Valley Baseline .............................................................................................................................................193
The Effects of Other Peak Processing Events on VB ............................................................................................195
Tutorial 6 Calibrating with an External Standard ..............................................................199

Overview.................................................................................................................................................................199
Generation of Calibration Data ...............................................................................................................................199
The Calibration Curve.............................................................................................................................................203
Tutorial 7 Calibrating with Internal Standards ..................................................................207

Overview.................................................................................................................................................................207
Generation of Calibration Data ...............................................................................................................................207
The Calibration Curve.............................................................................................................................................212
Using the Calibration Curve Options (Curve Manager)..........................................................................................214
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2000 GC/MS Application Notes ...........................................................................................221
Application Note Index............................................................................................................................................221
Advantage Note Index ............................................................................................................................................225
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Exercises
Overview
Varian MS Workstation controls and supports Varian ion trap and quadrupole
mass spectrometers. Several Workstation applications generate, process and
review Varian MS files.
Method Builder and System Control create MS data files in two formats (*.sms
and *.xms). MS Standard Reports and MS Custom Reports produce “Single
Run” reports for a data file. Use MS Data Review to view single and multiple
chromatograms, extract spectra, reprocess data files, view results and search
MS libraries. Each application has an entry under the MS Workstation program,
and an icon button on the Star Toolbar.
This Tutorial Manual demonstrates the MS Workstation capabilities. While these
procedures use the 2000 ion trap, you can adapt them to your Varian platform.
Executing Exercises
Follow these instructions either using a printed manual or using On-Line Help. If
you are using On-Line Help, you can use any of three methods to follow the
exercise instructions:
I. Print each exercise, then follow the printed instructions.
If you use at a lower screen resolution (800x600) use this method. When printing
topics that include graphics, you may need to adjust your printer’s properties to
use a fine dithering mode for graphics.
II. Alternate between Help and the Varian MS Workstation Application
Activate both a Varian MS Workstation application (such as MS Data Review,
System Control, or Method Builder) and the Exercises or other Tutorials. To
alternate between the instructions in the Exercise or Tutorial and the Varian MS
Workstation application, click on the desired application in the Windows
Taskbar (usually at the bottom of the screen). You may also use the keyboard
command <Alt +Tab> to alternate between applications and Help.
III. Split the screen between MS Data Review and its Help file.
1. Start MS Data Review.
2. Minimize or close all applications other than MS Data Review.
3. Push the ? button on the MS Data Review toolbar to load On-Line Help. Or,
use the Start button in the Windows Taskbar to open Help.
(Start >Programs >Varian WS >Documentation >MS 2000 Tutorial Help)
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4. Split the screen between any one of the Varian MS Workstation application
and its On-Line Help by right-clicking in an empty area on the Windows task
bar (the one containing the Windows Start button) and choosing Tile
Horizontally or Tile Vertically.
Running an MS Method without a GC Method

To run an MS method without a GC module or GC method, do the following:
From the System Control Menu, under Instrument, select Configuration.
Click on the GC Module icon and drag the icon from the Instrument area to the
Available Modules area. In addition, if you have an AutoSampler icon, drag it to
the Available Module area to deactivate it. This will disconnect the GC and the
Autosampler modules, and methods will not be downloaded to these modules
when an MS method is activated (if you have a CP-8400/8410 AutoSampler, you
only need to drag the GC icon as the CP-8400/8410 will be part of the GC Status
and Control screen). To activate the GC and Autosampler modules, drag the
icons back to the Instrument area of the Configuration screen.
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Executing Exercises
Loading an MS File in MS Data Review
Loading an MS File in MS Data Review

When MS Data Review is started, the Plot Chromatograms and Spectra window
is opened if “Plots” was selected under “View to Display on Start Up” in the MS
Data Review Application Preferences window (accessed from the menu
Preferences >Application Start Up).
If “Process” or “Results” was selected under “View to Display on Start Up,” the
Plot Chromatograms and Spectra window can be opened by choosing the Plot
Chromatogram and Spectra button on the MS Data Review toolbar. The

Plot Chromatograms and Spectra view displays a chromatogram window as well
as Data File and Plot Descriptors panes, which can be shown or hidden at
startup if “Show selection pane” is checked/unchecked in the MS Data Review
Application Preferences dialog. The Data file and Plot Descriptors panes can
also be shown/hidden by clicking the Tree button in the MS Data Review

toolbar.
Select a data file and a descriptor to display a chromatogram. For example, to

display the TIC (Total Ion Current) chromatogram for the 10_ng.sms file, select
C:\VarianWS\MSTutorials\10_ng.sms in the Data File Pane and TIC from the
Descriptor Pane.
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Use the Descriptors Pane to select chromatograms of specific scan functions
used in the data acquisition. In this example, the data file, 10_ng.sms, is a
calibration file, which used to quantify an unknown sample (see the Quantitation
Tutorial presented later in this Manual). The Descriptors are Method Descriptors,
which show the components of the compound table used in the quantitation
process. If you open this data file before using it in a calibration process, the
method descriptors are not listed in the “Descriptors Pane”. Select the
Descriptors you wish to display in the “Descriptors Pane” by right-clicking them.
You can also display Chromatograms by selecting File >Select Chromatogram
Data to Plot in the MS Data Review menu or the toolbar button.
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Executing Exercises
Displaying Mass Chromatograms
After selecting a file, click Add\Replace, then Open File(s). The RIC
(Reconstructed Ion Current) is displayed if RIC was selected in the Data column.
To display chromatograms generated by specific ions, see the topic “How to
Display Mass Chromatograms” below.
Opening an MS File from Windows Explorer

Locate data files in either *.ms, *.sms, or *.xms format using Windows Explorer.
Double-click on the desired file to open it in MS Data Review. Note that MS Data
Review may remain minimized in the Windows Taskbar. When you Restore MS
Data Review, the file you selected is displayed. You may also double-click a data
file received in an e-mail message to open it in MS Data Review.

To display chromatograms generated by specific ions, type the ion(s) m/z values
in the Ions box located at the lower corner of the chromatogram window, then
press Enter on the keyboard. When using the command File >Select
File/Chromatogram.. in the MS Data Review menu or the toolbar button,

the following options are available in the Data column besides the RIC value
(default):
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1. If no file is selected, select a file from the list and click Add\Replace.
2. In the Data column for the line corresponding to the desired file, click on the
down arrow at the right. This opens the list of options: RIC, Ion(s), etc.
3. Select Ion(s) and enter one or several. Repeat the process with other mass
combinations, exploring the options described. Note that you can also click
on the Edit Ions button to change the displayed mass chromatograms.
Displaying Multiple Chromatograms

Multiple data file chromatograms can be displayed by selecting the files in the
Data File pane while pressing the Ctrl key. Multiple chromatograms for different
plot descriptors can be displayed by selecting the plot descriptors in the
Descriptor Pane while pressing the Ctrl key. Selecting plot descriptors in the
Descriptor Pane while pressing the Shift key will display the chromatograms for
all plot descriptors listed between the selected ones.
1. Select the NEWINTERF15.XMS file in the C:\VarianWS\MSTutorials
directory in the Data File Pane. While pressing the Ctrl key select the
NEWINTERF16.XMS file in the same directory.
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Executing Exercises
2. While pressing the Ctrl key select different descriptors from the Descriptor
pane. Chromatograms corresponding to the selected plot descriptors and
data files are displayed simultaneously.
3. Check the box “S” at the bottom of the Plot Chromatograms and Spectra
window to select the “Segment” mode instead of Full chromatogram. You can
display different time segments by clicking the arrows below the
chromatogram window.
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4. Select the “f” button to sort the displayed chromatograms by “Files”.
5. Select the “p” button to sort the displayed chromatograms by Plot

Descriptors.
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Executing Exercises
Getting Spectra from an MS file
6. Use the toolbar button in the Plot Chromatograms and Spectra

window to switch between Stacked, Overlaid and Normalized Plots. You can
also select these options by using the command Chromatogram >Set
Chromatogram Display in the MS Data Review menu.
Alternatively, you can display multiple chromatograms by using the command
File >Select File/Chromatogram in the MS Data Review menu or the

toolbar button.
1. Select a file from the list and press the Add\Replace button twice to add the
same file for two displays. It’s preferable to work with the same data files as
in the first part of this tutorial (NEWINTERF15.XMS and
NEWINTERF16.XMS)
2. Select different ions in the Data column and plot descriptors or channels in
the Channels column for each line. Explore the Plot per Segment option in
the Channels column.
3. Select a different data file from the list and press Add\Replace twice to add
another file for multiple displays.
4. Make the same selections in the Data and Channels columns as in step 2.
5. You can explore the display options again (Segment mode, Sort by File or
Plot descriptors, Stacked/Overlaid/Normalized) as described in step 3-5 of
the first part of this tutorial.
Getting Spectra from an MS file

In the Chromatogram window, click on a point of interest in the chromatogram.
The corresponding spectrum will be displayed in a spectrum window (if the single
click action is set to Display Spectrum). You may refine the position of this
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spectrum by clicking again, or by using the arrow keys or the toolbar
buttons to move the pointer tight or left one scan at a time.
The Chromatogram >Set Spectra to Average command in the MS data Review
menu allows you to display an average of 1 (default), 3, 5, or 7 spectra.
Alternatively, you can use the button in the Chromatogram toolbar to
select the number of spectra to be averaged for display.
Spectra may also be background-corrected as described in the next topic,
Performing a Background Correction.
Performing a Background Correction

Load a file of interest and display its TIC or a mass chromatogram. In the
Chromatogram menu, verify that the item Show Background Correction
Markers is checked. Alternatively, you may show/hide the background correction
markers by using the toolbar button, or by right-clicking anywhere in the
chromatogram window, select Chromatogram Plot Preferences >Markers and
check/uncheck Show Background Correction Markers.
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Executing Exercises
Performing a Background Correction
Use the command Chromatogram >Edit Background Correction… to enter

the background selection mode.
You may also use the toolbar button .
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While the Background Correction for Plot 1 dialog is open, if you move the
mouse over the chromatogram, the cursor indicates that clicks of the mouse
will add background reference points.
Select an isolated peak (you may need to zoom in first) and click on the baseline
in front and in the back of the peak of interest.
Markers are added to the plot, indicating the location of the background
reference, the number of points averaged, and the baseline level for the plotted
abundance. Holding the mouse over one of these points changes the cursor to a
hand symbol. Using this “hand tool” you can fine-tune the selection of the
background point. After you close the background dialog (using the Done
button), the reference spectra you have chosen will be used for background-
correcting any spectra obtained from this plot.
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Executing Exercises
Performing a NIST Library Search
While the Background Correction dialog is displayed, you can delete all the
background spectra by using the Delete All button, or deleting individual spectra
by selecting the Delete mode and clicking on the reference spectra to delete.
The cursor indicates that clicks of the mouse will delete background
reference points. You can also move existing reference spectra by a click and
drag operation. This is done by positioning the mouse over the reference point so
that the hand tool appears, and then clicking and dragging the point to the
desired location.
Performing a NIST Library Search

NOTE: This is only available if you own the NIST PC Search program, Version
1.6 or higher.
Select Search > Library Manager . If no libraries are listed, click Initialize and
enter the path to your NIST libraries (typically C:\NIST02\MSSEARCH\). This
should result in MAINLIB and REPLIB being selected. Close the NIST Library
Manager by clicking Done.
You do not need to repeat the above step for subsequent searches.
After a spectrum of interest is displayed, press the Search toolbar button

in the MS Data Review window and select Library Search Active Spectrum.
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The Library Search a Spectrum window displays with a list of matches for the
searched spectrum. Press the button and select Spectrum Search.
The NIST Search for Target Spectrum dialog appears allowing you to change
the search parameters and/or edit constraints to better refine your library search.
Other searches (which are not based on a target spectrum) are also available.
Select Search >Library Search by in the MS Data Review menu. The following
search options are available:
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Executing Exercises
How to Create or Edit NIST libraries
How to Create or Edit NIST libraries

Select Search > Library Manager in the MS Data Review menu. This selection
opens the NIST Library Manager dialog.
To create a new NIST User Library, press the Create User Library button and
provide a new name for the library to be created (it is created as a sub-directory
of NISTMS).
To select an existing NIST User Library, click Add Library. The Select NIST
Library dialog opens. Click a library name from the list and press the Select
button.
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To edit a NIST library, click on the entry in the list and Edit Libraries. Click
Select to choose another library or access a given spectrum in a library. Use
Next & Previous to navigate sequentially the library. Use Edit to modify the
current spectrum. The spectrum is modified in memory, not in the library. You
may put the spectrum back in the same or another library. Use Delete to delete
the current spectrum. This function is only available in User Libraries. Press
Export >To NIST User Library to add the current spectrum (modified or not) to a
NIST User Library.
Building a Spectrum List

MS Data Review can build lists of spectra in an ASCII format. These lists can be
read by the NIST PC Search program. MS Data Review uses Spectrum Lists as
an input for searching chromatograms or spectra as well as in the quantitation
process.
1. Select Spectrum List >Create New Spectrum List. Type a name and
choose a location in the Create Spectrum List dialog that is opened and
press Save. A dialog window is opened that asks if you wish to “Make this
file the active file?” Press Yes.
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Executing Exercises
Building a Spectrum List
2. In the MS Data Review menu select Chromatogram >Set Single Click

Action >Export Spectrum to Active Spectrum List.
3. Click the scans of interest in the chromatogram window to add the selected
spectra to the active spectrum list.
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A spectrum list can also be generated by selecting Spectrum List >Build
Spectrum List From Active Chromatogram in the MS data Review menu. This
command opens the Edit Integration Parameters dialog.
Press the Help button in the Edit Integration Parameters window to find the
significance of the fields and buttons in this dialog and how are they used to
make a spectrum list. Use the default values and press OK. The spectrum list is
displayed as well as a spectrum window for visualizing each spectrum in the list.
Explore the influence of different integration parameters values in the peak
detection process performed to build the list.
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Executing Exercises
Editing Spectra
Hold the cursor over any button in the Spectrum List toolbar to display a
description..
Select the Library Search Spectrum List button and then save the search
results by pressing the Update all Searches with Matches button .
You can add spectra by using the Add Spectrum button and you can delete
spectra by using the Delete Spectrum button .
Editing Spectra
Select a peak in the Chromatogram window so that a mass spectrum is shown in
the Spectrum display. Use the menu command Spectrum >Edit Active
Spectrum.
This opens the Edit Spectrum dialog.
To edit an attribute (name, comment, formula, molecular weight, CAS number,

Base Peak), enter the information in the desired field.
To edit mass-intensity pairs, use the Add\Replace and Delete buttons.
Press Save to accept the changes or Cancel to reject them.
The changes are now reflected in the Spectrum window.
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NOTE: Making a change to the ion intensity pairs will flag the spectrum as edited
with a ‘(E)’ designation in the spectrum header.
The edited spectrum may now be exported to NIST User Libraries, to a Spectrum
List or text file.
Printing Pictures
Print commands can be issued from the file menu and many windows.
1. Display a spectrum by clicking on a scan of interest in the chromatogram
window.
2. In the File menu of MS Data Review window select Preview Reports.
3. In the MS Data Review menu select File >Print… .This command opens the
Make Reports dialog. Select Print Active Chromatogram in the list and click
Print.
The printout is shown in a preview window that allows you to print, delete or
export the page.
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Executing Exercises
Exporting Pictures
To close the Preview window, click the close box (X) in the upper right corner, or
click the Exit command in the menu.
If Preview Reports and Send Reports to Spooler File are both unchecked, the
Print commands sends the files to the printer.
You can also choose to print the active chromatogram and spectrum plot by
right-clicking in the chromatogram/spectrum window.
Exporting Pictures
You can exporting to the Clipboard or Picture File to import plots and spectra into
third-party word processing and graphics programs. Right click in the
chromatogram window and select Export >Chromatogram Pane >Picture File
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Select a Directory and Filename for the picture you want to export. Click OK after
making the name and directory selection.
Insert the picture in a Microsoft Word™ document using the Insert >Picture
>From File The Picture format (vector graphics) leads to much better graphics
than the Bitmap format (raster graphics).
Creating and Using a Spooler File

In addition to printing individual reports from Chromatogram, Spectrum, Library
Search, and other windows in MS Data Review, the user may also create master
files called Spooler Files (also referred to as Reports Files). A Spooler File is a
collection of printouts from various screens within the MS Data Review
application. Files may contain copies of any screen, which may be printed from
MS Data Review.
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Executing Exercises
Creating and Using a Spooler File
NOTE: Reports are automatically added to the active Spooler File when the
Send Reports to Spooler File is checked in the MS Data Review File menu
AND the user selects a print command from the MS Data Review File menu. You
may add reports to the Spooler File without printing by simply clicking Exit in the
Active Spooler File screen (opened with the command File >View Spooler File
in the MS Data Review menu). You may stop the automatic additions to the
Spooler File by deselecting the File >Send Reports to Spooler File command.
1. To create a Spooler File, open a data file in MS Data Review. Use the
command File >Select Spooler File in the MS Data Review menu. You will
be prompted to choose a name for the new Spooler File or to open an
existing one.
2. Select File >Send Reports to Spooler File.
3. Select a spectrum from the active chromatogram. Use the menu commands
File >Print to add entries to this Spooler File. In the Make Reports window
select Print Active Chromatogram and Spectrum Plots and click Print.
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4. To review the Spooler File contents, use the menu command File >View
Spooler File. The last report added to the Spooler File is always shown
when the View Spooler File option is chosen. Use the Next/Previous Page
menu commands to navigate the Spooler File. You can click and drag within
the page to get a closer view of details.
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Executing Exercises
Exporting Spectra
5. If you want to add reports to the Spooler File without printing any of the
pages, click Exit in the Active Spooler File menu.
6. You can print the current page, the current report or the all reports by using
the print icons in the toolbar.
Exporting Spectra
Click on a point of interest in the chromatogram plot to display a spectrum.
Click on the Export Chromatograms and Spectra button in the MS Data

Review toolbar and select Active Spectrum. You can then make the export
destination selection.
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Displaying and Printing Log Information
The Log is the section of the data file, which documents the instrument hardware
and MS acquisition parameters. This is where you can find out exactly how the
data file was acquired. The log information can also be viewed in the data
acquisition method used to acquire the file.
In order to view the Log from a plot in MS Data Review, the acquisition segment
information needs to be showing on the bottom of the plot window. This is
enabled by default, but if it is not showing you will need to right click anywhere in
the chromatogram plot and choose the Chromatogram Plot Preferences, make
sure that the Show Acquisition Segments item is checked.
A graphical representation of the acquisition segments is displayed at the bottom

of the Chromatogram window.
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Displaying and Printing Log Information
Place the cursor on this control (the cursor will add a “Log” label), to display log
components for the relevant segment.
If multiple plots are displayed, the Segments control refers only to the active plot.
Click on or below the segment bar in the chromatogram plot. The Data File
Information window will be opened.
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You can also obtain file information by right-clicking on a file name in the Data
File Pane and selecting Information >Show File Information.
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Acquiring a 2000 MS Data File
Introduction
This tutorial will familiarize you with the basic operation of the 2000 GC/MS
system, including the Varian MS Workstation environment, instrument setup and
tuning, GC/MS method building, and acquiring a data file. The GC column used
for this tutorial is a fused-silica 30m x 0.25mm ID, 0.25um phase coating of CP-
Sil 8 CB (Varian part number CP8751). The VF-5 MS factorFOUR column will
give similar results (Varian part number CP8944).The sample used in this tutorial
is the Column Test Mix (Varian part number 03-920273-00).
Starting the Varian MS Workstation

To set up the 2000 for acquiring a sample, you should first enter System Control
and tune the mass spectrometer. Your Varian MS Workstation software has
probably been installed so that the Workstation Toolbar appears at the top of the
screen. The Workstation Toolbar is a set of shortcuts to help you navigate the
Varian MS Workstation.
If the Toolbar is not present, open it from the following location: Start >Programs
>MS Workstation >Workstation Toolbar. Hold the mouse cursor over each of
the buttons in the Workstation Toolbar to display a tool-tip description. You can
find more options and complete descriptions in the Help on Star Toolbar
accessed by right-clicking in the free area on the right side of the Workstation
Toolbar. Click on the System Control button on the far left to enter System
Control. You may wish to choose the option Small Buttons on Toolbar so that
the Workstation Toolbar will occupy less space on the screen.
Setting Instrument Configuration for Manual Injections

After System Control is started, a new window opens. The components of the
System Control window vary depending on the mode of operation. The System
Control window title bar (the blue area at the top of the window) should read
System Control - Configuration.
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If this is not the active window, click Instrument >Configuration to open the
Configuration window.
The available instrument modules are shown at the bottom of the System Control
Configuration window. The Configuration window shown above indicates that a
3800 GC, a 2000 MS, and a Combi PAL AutoSampler are installed because their
Module icons can be observed in the window. For this tutorial we wish to perform
manual injections, therefore if you are using a Combi PAL or CP-8400/8410
AutoSampler, you will need to choose the manual injection selection in the Inject
Single Sample Dialogue or the Sample List dialogue. This selection is under the
Injector Mode selection of the respective tables and is labeled “Manual Injection”
or “Manual”. If you are using a 8200 AutoSampler, to configure the instrument for
manual injections, use the mouse to click on the 8200 Module (if it is present on
your instrument) and drag it into the Available Modules field at the bottom of the
System Control window.
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Setting Instrument Configuration for Manual Injections

To run an MS method without the GC module or GC method, highlight
Configuration under the Instrument menu and click the GC Module icon and
drag it from mid screen to below the bar labeled Available Modules.
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If you have a 8200 AutoSampler, drag and drop the Autosampler icon to the
Available module area (note that the CP-8400/8410 is controlled and displayed
through the GC Status and Control screen; it requires no special treatment). This
removes the GC and the AutoSampler modules from the instrument, and the
methods is not downloaded when an MS method is activated. To restore the GC
and Autosampler modules, move the icons back into the active field.
Adjusting and Tuning the 2000

To adjust and tune the 2000 MS, display the 2000 Module window by double-
clicking the instrument area background or using the Instrument menu to select
Varian GC/MS #1.
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The window titled “System Control - Varian GC/MS #1” will appear. The 2000
Module Window appears directly within it. If it is iconized, double-click to open it.
There are six different modes of operation. By default, the Manual Control mode
is active when you enter System Control. Other screens will appear when Auto
Tune, Temperatures, Diagnostics, Shutdown, and Acquisition buttons are
clicked. Note that the System Control and 2000.40 (2000 MS module) title bars
both show Not Ready.
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Adjusting RF Tuning
If you are not already in the Manual Control section, click it. The first operation
is Adjust RF Tuning. This adjustment is performed by first clicking the
Adjustments tab and then selecting the Adjust RF Tuning button.
If the RF Ramp is not passing test requirements, open the front door of the MS
and find the labeled RF Adjustment screw and adjust it with a flat-blade
screwdriver while observing the feedback on the screen. When the Control and
Status message reads “RF Response is Within Limits”, click Save.
Adjusting Calibration Gas

Next, click Adjust Cal Gas. Open the front door of the 2000 MS and use the
Calibration Gas needle valve to bring the Cal Gas status to OK. Note that the
acceptable range corresponds to an Ion Time (seen in the Operating Conditions
field on the right side of the dialog) of between 300-1000 µSec. When the test
passes, click on Done to exit the adjustment.
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Adjusting CI Reagent
Adjusting CI Reagent
Click Adjust in the CI Reagent area. Select the CI gas that your instrument is
using by clicking the arrow. Open the front door of the 2000 MS and use the CI
Gas needle valve to bring CI reagent status to OK. After the test passes, click
Save Results.
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Running Auto Tune
Setting GC Column Temperature for Mass Calibration
Data is usually acquired with a constant flow of about 1mL/min through the GC
column. However, some applications require a constant pressure injection and a
temperature increase over time. In the constant pressure mode, the column flow
rate will decrease as column temperature increases during the run. This will
cause a slight shift in the mass axis for the collection of GC/MS data. To assure
correct mass assignments, always run Mass Calibration with the GC Column
Oven set at or near the high temperature for the column program in your GC/MS
method. You can program the temperature from the GC Method (using Method
Builder or the GC keyboard). For this tutorial use a constant flow of 1mL/min.
Choosing Auto Tune Methods

Click Auto Tune. Click on the items Air/Water Check, Electron Multiplier Tune,
and FC43 Mass Calibration. It is not necessary to run the Trap Function
Calibration method unless you wish to perform MS/MS or SIS types of
acquisitions. Click on Start Auto Tune to run the specified suite of tuning
procedures.
After Auto Tune has started, the following windows should appear:
When the Air/Water check completes, the Multiplier Tune and Mass Calibration
methods will be run automatically unless you have selected “Single Step” in the
checkbox below. In “Single Step” mode, the tuning will pause between Auto Tune
steps so that you may examine the results of each test and then click the
Continue button in the Status and Control field to initiate the next Auto Tune
procedure.
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Examining Current Module Attributes
NOTE: The Air/Water Check will use the last 105 Electron Multiplier Setting and
not the manual setting. If the electron multiplier is replaced, the Electron
Multiplier Tune procedure must be done before the Air/Water Check.
Troubleshooting (Optional)
If any of the steps in the automatic tuning fails, the problem should be corrected
before running the tuning procedure again. The system should never be
operated if the Air/Water check fails. If in doubt, consult the procedure How to
Check for Leaks in the 2000 GC/MS Hardware Maintenance Manual or Help File,
both of which contain many procedures to assist you in troubleshooting
problems.
NOTE: It is a good idea to become familiar with the advice available in the
Troubleshooting section of the 2000 GC/MS Hardware Maintenance Manual or
Help File.
Required Frequency of Tuning

On a daily basis, the only tuning checks that need to be made are (1) Air/Water
and (2) Mass Calibration. The electron multiplier voltage setting should be
checked biweekly.
NOTE: The RF voltage ramp should be checked and adjusted, if needed,

whenever the trap temperature is changed. Mass calibration should be run again
after any adjustment of RF Ramp and/or ion trap temperature. To optimize mass
axis stability, mass calibration should be run with the GC column oven at or near
the maximum temperature for planned GC/MS runs. However, this precaution is
not required if the GC is run in Constant Flow mode.
Examining Current Module Attributes

Note the combo box next to the Show/Hide Keypad button in the Auto Tune
dialog box.
The Current Module Attributes section of the display shows the current settings
and tune status of the instrument. This information is also added to the Segment
Log for all acquired data files. Therefore, you can verify before a run, or in
examining past archived data files, that the instrument tune is valid.
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Preparing a GC/MS Acquisition Method
Creating a New Method

You may build and edit GC/MS Methods in the Method Builder application. To
begin this process, click on the Method Builder button in the Toolbar.
The following dialog box will appear. Choose Create a New Method File and
click OK.
Choose Instrument 1 and click Next in the Select Configuration window.
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If the GC was removed from the instrument, it won’t be displayed as part of

Instrument #1. Refer back to Setting Instrument Configuration for Manual
Injections earlier in this tutorial section to reconfigure the GC as part of the
Instrument.
Select only 2000 Mass Spec as the detector and click Next.
NOTE: If you were to acquire data with a standard GC detector such as an FID,
PFPD, or ECD, you would select the GC detector module here.
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Select only “Channel 1=MS Data” and MS Data Handling for this tutorial, then
click Next.
NOTE: The MS Data Handling section would be added to perform post-run

processing of data files, including Quantitation and automated generation of
Custom Reports.
The Confirm Configuration dialog shows that you will create the new method
with sections for 3800 GC control and 2000 MS control.
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Now click Finish and the Method Builder dialog box will open with a directory
tree on the left side showing an outline of the sections available for editing.
Editing the Data Handling section will be discussed later in this manual in the
Quantitation tutorial. Before you begin editing the method, use the menu
command File >Save As to save the method to the name Coltest1.mth. Enter
the name Coltest1 in the file name field and click Save.
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Editing the Method
Selecting and Editing the MS Method Section
You are now ready to edit the method so that you can acquire a data file with the
Column Test Mix sample. Notice that as you highlight different items in the
Method Directory, different screens appear in the right section of the window.
Under the Method Directory item 2000 Mass Spec Control, click on the item MS
Method Editor. The display on the right will now show the MS method.
Note that you may click and drag on the splitter bar separating the Method
Directory from the Method Display and adjust the position so that the entire MS
Method is visible on the screen. Alternatively you may click on the Show/Hide
Method Directory button in the Method Builder toolbar to hide the Method
Directory. The top area of the method screen shows a table of segments for the
acquisition.
The default table for a new MS section consists of two segments. The first
segment is a Filament/Multiplier Delay segment for the first three minutes
(Ionization Mode = None). This segment will be acquired with the filament and
multiplier turned off to protect the instrument until after the elution of the solvent
peak.
The second default segment from 3.00 to 10.00 minutes is Electron Ionization
with Automatic Gain Control (EI Auto) to acquire MS data over the m/z range 40-
650. This is the standard ionization mode for full-scan EI acquisitions. If you
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Editing the Method
highlight a cell in Segment 2 of the Segment Table, you will see additional tab
dialogs for Segment Setpoints and Ionization Mode.
Examine the parameters which may be adjusted in the Segment Setpoints

dialog but do not change them at this time. Click on the tab dialog Ionization
Mode - EI Auto to see the parameters that may be adjusted there. If you would
like more details on the adjustment of these parameters, go to the section
Editing an MS Method in the MSWS Software Reference Manual.
To prepare the MS section of the method for acquiring the Column Test Mix
sample, change the end time for Segment 1 by highlighting the End (min.) cell
and entering 4.00. Then highlight the Segment Description cell for Segment 2
and type in “coltest”. Change the end time for Segment 2 to 19 minutes, and then
change the m/z range to 40-350. Now the screen should look like the following:
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Selecting and Editing the GC Method Section
NOTE: This tutorial assumes that you have a 3800 GC. 3900 GC programming
is similar.
After completing your examination of the MS section of the method, click on the
Injector section of GC Control in the Method Directory. (If you have used the
Show/Hide Directory button in the toolbar to hide the Method Directory, click on
the button to make the directory appear again.)
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Editing the Method
The Injector section of the 3800 GC method will appear. The tab dialog for the
Front injector is shown by default. If your GC column is installed to the Middle or
Rear injector positions, click on the appropriate tab and modify the method so
that the injector temperature is set correctly.
Set the injector temperature to 250 °C. You may also set the Split Ratio in this
section. Click on Split Ratio tab and enter the values shown below:
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Now click on the Flow/Pressure section of the Method Directory. Select the
Front, Middle, or Rear Injector, depending upon where your column is installed.
Note that the method is set up for a Type 1 Electronic Flow Control (EFC) in the
Front Injector. You may need to modify the EFC Type to match your instrument
configuration. The usual mode of acquiring data is constant flow. This can be
done by selecting On in the Constant Column Flow Mode field at the bottom of
this dialog. If you wish to use constant flow, choose a flow of 1mL/min.
After examining and editing the Flow/Pressure section, click on the Column
Oven section in the Method Directory. Set the Stabilization Time to 0.50 minutes
and set up the Column Temperature Program Table as shown next.
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Starting the Acquisition
Activating the GC/MS Method
You have now completed the examination and editing of the method
Coltest1.mth. To Save the method use the pull-down menu File >Save. After the
method has been saved exit the Method Builder with the menu command File
>Exit or click on the X button in the upper right corner of the Method Builder
window.
Activating the GC/MS Method

If System Control is not open, start the application from the Workstation Toolbar.
If System Control application opens the Configuration window, select 1:Varian
GC/MS #1 from the Instrument menu.
Use the menu command File >Activate Method to display the file selection
dialog. Highlight the method Coltest1.mth and click Open. The GC and MS
portions of the method will be downloaded to the instrument.
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Starting the GC/MS Run
Although you could construct a Sample List and run several samples in
Automation, for this tutorial you will learn how to quickly run one sample at a
time. When you see the 2000 module come into the Ready state. Click on the
Inject >Inject Single Sample option.
The Instrument 1 Parameters dialog box should appear. Enter your name or
initials in the Operator field and Click the OK button.
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Starting the GC/MS Run
The Inject Single Sample dialog should appear.
The active method is displayed in the field Inject the Sample using the Method.
Type in a name for your sample in the Sample Name field. Here we have just
chosen the name column test. After typing the name, you can activate the Data
Files button by clicking in any other field. Click on the Data Files…. button to
open the Data File Generation dialog.
In this dialog, you can choose a directory where you want to save the data file
and select the symbols for the labels you want to be added as extensions to the
file name.
After you making the file name selections, click the Inject button in the lower left
of the dialog. Make sure the 2000 MS Module screen is shown (not the GC
Module). Verify in the Control and Status area that the 2000 status is “Ready”
and “No Faults”.
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You may also use the Windows menu to check the status of the GC module as
well. While the GC injector and column temperatures are being adjusted to those
set in the method, the GC module status will be “Equilibrating”.
When the GC has equilibrated and stabilized, the Status Indicator in the System
Control Toolbar should read Waiting for Injection of Sample. Choose the
option Chromatogram Only for the display.
Injecting 1 µL of the Column Test Mixture

Rinse a 10 µL syringe in hexane and expel air bubbles by pumping the syringe
plunger up and down several times. Pull the syringe up to the 1.0µL mark to
create an upper air gap. Place the needle in the Column Test Mix solution and
draw the plunger up to the 2.0 µL mark. Finally, remove the syringe from the
solution and draw the plunger up a further 1.0 µL. You can now see exactly how
much sample solution is in the syringe. There should be approximately 1.0 µL of
air above the sample and 1.0 µL of sample in the barrel of the syringe.
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Monitoring Data Acquisition in Progress from System Control
The syringe needle should be left in the injector for 2-3 seconds before
depressing the plunger. Inject the sample using an even, consistent injection
speed. The optimum speed is about 1 µL/second. As soon as the automatic start
switch on the GC injector is depressed, the acquisition will start and you will
observe the acquisition of the data file column test.sms has begun.
Monitoring Data Acquisition in Progress from System

Control
The MS method has specified a 4.00 minute Filament/Multiplier Delay, so,
although the chromatogram appears in the display window, there are no peaks
observed at first.
Examine the features of the 2000 Module during the initial segment. Note that the
Status Indicator in System Control now indicates Running. In the Control and
Status region, note the progress of the Runtime indicator. In the MS Method
region, note the information associated with Segment 1. Now observe the Data
File name, Scan Number, Ion Time, and Ion Count in the Operating Conditions
region. Click on the Hide Keypad button to get a full-screen display of the
chromatogram. Click on the Show Keypad button to display the keypad again.
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When the Runtime reaches 4.0 minutes, Segment 2 will be downloaded and
acquisition will switch to EI-Auto mode. Again note the information displayed in
the MS Method and Operating Conditions regions. Move the mouse over the
buttons in the display toolbars and examine the options available. Choose the
Time Select button in the Chromatogram toolbar. This button allows you to
display the mass spectrum of a particular peak in the chromatogram. You may
also click and drag in the chromatogram display to expand a given area for
careful examination.
You may look at both the Spectrum and Chromatogram by selecting that option
from the drop-down list box.
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Monitoring the Acquisition in Progress from MS Data Review
Monitoring the Acquisition in Progress from MS Data

Review
Viewing the Chromatogram
The last button on the right of the Chromatogram toolbar in System Control
opens MS Data Review . When this option is chosen the MS Data Review
application opens and the file currently being acquired can be displayed and
used for qualitative analysis. Click on this button now to open the Plot
Chromatograms and Spectra view of MS Data Review.
NOTE: The System Control application will remain open and accessible while
you are viewing data in MS Data Review. You can return at any time to System
Control by Restoring its minimized display from the Windows Taskbar or by
clicking <Alt +Tab> on the keyboard until System Control is selected.
You will see that the Chromatogram display is set for the full time length of the
current method but that only the first portion of the run has been completed. The
display is updated every few seconds with additional scans.
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Displaying Mass Spectra Peaks of Interest
As you did in the Acquisition dialog in System Control, click on a peak of interest
to display the mass spectrum. The MS Data Review spectrum display appears
with its own toolbar for user adjustments.
Performing Library Searches

Now that a spectrum has been selected, you can library search it by selecting
Search >Library Search a Spectrum >1A in the MS Data Review menu. You
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Setting Instrument Configuration for Automated Injections
Configuring the Instrument
can quickly Library Search other spectra by holding down the ‘L’ key on the
keyboard while clicking on a peak in the displayed plot.
You can examine and print library search results during data file acquisition. All
of the library searching and other Qualitative Identification procedures possible
within MS Data Review are discussed in the tutorial “Qualitative Analysis of
GC/MS Data”.
Retention Times for Analytes in the Column Test Mix

Sample
If you wish to perform further qualitative analysis on this data file, you may open
it again with MS Data Review at a later time. The components of the Column test
mix and their approximate retention times are shown below.
Compound Retention (min)

Decane 9.063
1-Octanol 10.408
Undecane 10.849
Nonanal 10.966
Phenol, 2,6-dimethyl- 11.074
Quinoline, 1,2,3,4-tetrahydro- 11.457
Benzenamine, 2,6-dimethyl- 12.167
Decanoic acid, methyl ester 14.117
Undecanoic acid methyl ester 15.183
Cyclohexanamine, N-cyclohexyl- 15.275
Dodecanoic acid, methyl ester 16.025
Benzene, hexachloro- 17.667

Details on Configuration setup are available in the 2000 Operational Manual. A
portion of that information is given here. Before you configure your instrument
make sure that required instrument modules are enabled: right click to the right
side of the method Quick Link button in the Workstation Toolbar and select
Enable/Disable Instrument Modules.
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If for example you have a 3800 GC and a Combi PAL AutoSampler, enable the
3800 GC and the Combi PAL AutoSampler. (For users who have a CP-
8400/8410 AutoSampler, the autosampler is controlled and displayed through the
3800 or 3900 Status and Control screen. Thus, only the GC needs to be
enabled.) When the desired configuration is enabled, click on OK and open
System Control.
If the instrument has not been previously configured, the 2000, 3800 or 3900
GC, and the Combi PAL AutoSampler (if it exists in your system) will appear at
the bottom of this screen in the “Available Modules” section of the window. Use
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the mouse to click and drag the icons into the center of the screen. If the
Combi PAL icon is present, drag it into the AutoStart Module. The 2000 and
3800 icons go anywhere to the right of the box, but not in the AutoStart Module
box.
NOTE: If an 8400/8410 AutoSampler is attached to a GC, the GC module should

be placed in the AutoStart Module.
Once the modules are in place you are ready to proceed.

The AutoSampler is controlled by the parameters set in the Method, which can
be opened by clicking on the Method button in the system control screen.
Clicking on the AutoSampler section in the Method Directory
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Clicking on the Configuration section will give you a screen similar to the
following.
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Creating the Sample List
This screen shows parameters for a Combi PAL injection, which can be modified
according to the specific applications. Once having the injection parameters set,
save the method and open the System Control application. If you are in the
Configuration mode, select the Instrument menu and click on 1: Varian
GC/MS #1 to open the modules control windows.
Activate the method that you are going to use for the AutoSampler, GC and MS
using the menu command File >Activate, select the method and then click
Open.
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Use the menu command File >New Sample List in System Control to create a
Sample List.
A file selection dialog will be displayed. Type the name “automation” in the File
Name field and click on Save.
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The following screen will be displayed.
Add the samples you wish to run to this list. Type in sample name and vial
position information for your samples. Use the pull down arrow to select Analysis
under Sample Type.
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To start automation, click on the Begin button in the bottom left corner. The
autosampler will inject the sample contained in vial position 1, followed by the
samples in positions 2 and 3.
.
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Qualitative Analysis of GC/MS Data
Analyzing GC/MS Data

Qualitative analysis to identify compounds present in a data file is one of the
most common exercises performed by a GC/MS user. This tutorial will show you
some of the basic operations that can be performed with the 2000 software to
assist you in this task. The data file you will use for this exercise is found in the
directory C:\VarianWS\MSTutorials. The files in this directory are also used in the
tutorial Quantitative Analysis of GC/MS Data.
This tutorial is designed to run with the data file 80_ng.sms and the user library
tutorial.lbr. The data files are extracts from chromatograms for semivolatile
compounds run by split injection on the 2000 GC/MS.
Demonstration Files
The following extracted data files are present in the directory
C:\VarianWS\MSTutorials:
10_ng.sms 80_ng.sms
20_ng.sms 120_ng.sms
50ng_ccc.sms 200_ng.sms
The files contain data on the following nine analytes.
Compound Retention Time(min)

2,4-Dimethylphenol 7.32
bis(2-Chloroethoxy)methane 7.61
Benzoic acid 7.67
2,4-Dichlorophenol 7.75
1,2,4-Trichlorobenzene 7.98
Naphthalene-d8 (Internal Standard) 8.07
Naphthalene 8.13
4-Chloroaniline 8.48
Hexachlorobutadiene 8.72
This set of compounds has been chosen to illustrate the principles of GC/MS
qualitative identification as applied to real analytical results. For example,
benzoic acid coelutes with bis(2-Chloroethoxy)methane and is poorly focused
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(because the DB-5 column used in the analysis is inappropriate for free acids).
We will demonstrate in the tutorials how to deal with coeluting peaks to obtain
clean mass spectra for library searching.
The concentration of the internal standard compound (naphthalene-d8) is
40 ng/µL in all data files, whereas the concentrations of the other analytes is
indicated by the data file name.
To assist in qualitative identification of compounds in the data files, use the user
library file, Tutorial.lbr, which is located in the directory C:\NIST02\MSSEARCH.
Displaying a Data File

Open the MS Data Review application by clicking the MS Data Review button
on the MS Workstation Toolbar. The Plot Chromatograms and Spectra

window will appear on the screen. Select the C:\VarianWS\MSTutorial directory.
Select the file 80_ng.sms and click to open it.
Notice that there are two toolbars in this display. The one on top is referred to as
the MS Data Review toolbar. The lower toolbar is called the Chromatogram
toolbar. If you are not yet familiar with the options in the Chromatogram toolbar,
explore some of these features by holding the mouse cursor over each button
and observing the tool-tip descriptions. You can select to show/hide the gain
control and/or the acquisition segments by right-clicking in the

chromatogram plot and choosing Chromatogram Plot Preferences. The
Chromatogram Plot Preferences dialog opens where you can check/uncheck
Show Gain Control and Show Acquisition Segments. Explore the other plot
options that you can control in this dialog. Select Zoom Chromatogram as the
Click and Drag Action and expand a portion of the chromatogram by clicking and
dragging with the mouse. Place the cursor on each axis (you will see that the
cursor symbol becomes a double arrow) and double click to restore the full scale
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Background Correction
on each axis. You can use the Full Scale button to restore the full scale on
both axis.
Choosing a Mass Spectrum

Click on the first peak in the chromatogram. The mass spectrum of the scan you
selected is now displayed along with the chromatogram.
Background Correction
Background correction is a technique used to remove unwanted chemical
background ions from a target spectrum to ensure that a more accurate Library
Search can be run. Background points can be selected either manually or
automatically; both procedures are accessible from the MS Data Review
Window. First, make sure that Background Correct Spectra option is turned
“ON” under the Spectrum menu in the MS Data Review window.
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Alternatively, you can activate the Show Background Correction Markers
button in the chromatogram toolbar. Select the command Chromatogram
>Edit Background Correction in the MS Data Review menu. The Background
Correction for Plot 1 dialog opens and you can select to do a manual
background correction or an automatic one. This process was also described in
the How to Perform a Background Correction exercise earlier in this Tutorial
Manual. Select the Auto Background Correction tab for this tutorial and then
click Done.
Select a peak of interest in the chromatogram for which you would like to see a
spectrum. The label (BC) appears at the end of the scan specifications,
displayed in the upper right corner of the spectrum window, indicating that a
background corrected spectrum is displayed.
Running a Library Search on a Single Spectrum

Use the MS Data Review menu command Search >Select Search Libraries to
open the NIST Library Manager dialog. Use the Add Library button to add the
library, Tutorial.lbr. Inactivate any other libraries in the list. Click on Done to
return to the MS Data Review window. Click on the Search button and
select Library Search Active Spectrum. The results are displayed in the
Library Search a Spectrum window.
NOTE: You can quickly Library Search other spectra by holding down the ‘L’ key
on the keyboard while clicking on a peak in the displayed plot.
The following screen shows library search results for the first peak in the
80_ng.sms file.
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Running a Library Search on a Single Spectrum
When you select different matches in the list, a spectrum for each match is
updated in the spectrum window below the list.
You can repeat the search and edit constraints or change the parameters that
affect the identification process by clicking on the Do NIST Search button

and selecting Spectrum Search. This will open the NIST Search for Target
Spectrum dialog.
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Creating a Spectrum List
In the MS Data Review menu select Spectrum List >Create New Spectrum
List. This command opens the Create Spectrum List dialog for typing the
spectrum list file name and selecting the directory where it will be saved. When
saving the newly created spectrum list you will be asked if you want to make this
file the active file. Click Yes.
You can build the spectrum list automatically by selecting the command
Spectrum List >Build Spectrum List from Active Chromatogram as
described earlier in this manual in the How to Build a Spectrum List exercise.
You can also add spectra to the spectrum list one by one by selecting the peaks
of interest in the active chromatogram. In the MS Data Review menu select
Chromatogram >Set Single Click Action >Export Spectrum to Active
Spectrum List.
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Library Searching a Spectrum List
Click on the first chromatogram peak in the 80_ng.sms. file. The spectrum
corresponding to the selected scan is added to the active spectrum list. Similarly,
you can add spectra corresponding to all peaks of interest to the active spectrum
list. Now that you have created a List file, you can (1) library-search the
compounds in the list, (2) search another chromatogram for the presence of
those compounds. To stop adding peaks to the active spectrum list, select
another Single Click Action, such as Display Spectrum.
Library Searching a Spectrum List

After all scans of interest were added to the spectrum list, perform a library
search of the active spectrum list. In the Spectrum List window select the Library
Search Spectrum List button . The NIST Search for Target Spectrum
dialog opens. Use the default values and click Search. The search results are
displayed in the Spectrum List window. To save the search results in the
spectrum list, click the Update all Searches with Matches button .
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Use the up and down arrows to highlight entries in the table and to examine the
mass spectra. Note that you can adjust the splitter bar separating the display
areas to size the fields to your preference.
Performing a Chromatogram Search with a Spectrum

List
Once a Spectrum List has been created from a calibration data file, you can use
the list to quickly determine whether those compounds are present in a GC/MS
data file of an unknown. Choose the file 10_ng.sms to be the unknown
chromatogram, because this chromatogram also contains the nine analytes in
the list you have just created, but at different concentration levels.
Use the menu command Search >Target List Search a Chromatogram
>Select a Data File… This command will open the dialog Select Data File for
selecting the chromatogram that you want to search. Select the file 10_ng.sms
and click the Open File button. The dialog Target List Search Chromatogram
appears.
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Performing a Chromatogram Search with a Spectrum List
In the Target List Files click the Edit Target List button. This will open the
Spectrum List Manager dialog from which you can select the list(s) used to
search the chromatogram.
Use the Add File and/or Remove File buttons as needed so that you select only
the spectrum list previously created from the chromatogram file 80_ng.sms (the
spectrum list file is 80_ng.msp). After you select the spectrum list, click Done and
then Search in the Target List Search Chromatogram dialog.
The results will appear in the Target List Search a Chromatogram window.
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Highlight a peak in the list and observe the mass spectrum and the peak location
in the displays below. Use Next and Previous buttons to navigate the list.
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Quantitative Analysis of GC/MS
Data
Overview of the Quantitative Analysis Tutorials

This section contains eight tutorials which illustrate the concepts of quantitation
on the 2000 GC/MS system. The tutorials have been designed to run with a set
of data files and the user library Tutorial.lbr. The data files are extracts from
chromatograms for semivolatile compounds run by split injection on the 2000
GC/MS. The same data files are used repeatedly to demonstrate different steps
in the quantitation process.
Use the tutorials along with the text of Quantitation in the 2000 Software
Reference Manual to learn how each step of the quantitation process on the
2000 GC/MS is carried out.
Demonstration Files
The following extracted data files are present in the directory
C:\VarianWS\MSTutorials.
10_ng.sms 80_ng.sms
50_ccc.sms 200_ng.sms
These data files contain an extracted portion of chromatograms which contain
data on the following nine analytes. The identities of the analytes and their
retention times (in the 80_ng.sms file) are shown below.
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Table of Analytes
Compound Retention Time (min)

2,4-Dimethylphenol 7.32
bis(2-Chloroethoxy)methane 7.61
Benzoic acid 7.67
2,4-Dichlorophenol 7.75
1,2,4-Trichlorobenzene 7.98
Naphthalene-d8 (Internal Standard) 8.07
Naphthalene 8.13
4-Chloroaniline 8.48
Hexachlorobutadiene 8.72
This set of compounds has been chosen to illustrate the principles of GC/MS
quantitation as applied to real analytical results. For example, benzoic acid
coelutes with bis(2-Chloroethoxy)methane and is poorly focused (because the
DB-5 column used in the analysis is inappropriate for free acids). We will
demonstrate in the tutorials how to deal with coeluting peaks to obtain accurate
quantitation results.
The concentration of the internal standard compound (naphthalene-d8) is
40 ng/µL in all data files, whereas the concentrations of the other analytes vary
from 10 ng/µL up to 200 ng/µL, as indicated by the data file name. The inclusion
of the internal standard at constant concentration allows us to build an internal
standard calibration curve.
To assist in qualitative identification of compounds in the data files, use the user
library file Tutorial.lbr which is located in the directory C:\NIST02\MSSEARCH\.
Tutorial Topics
The topics covered in this tutorial section are:
• Qualitative Identification
• Building a Data Handling Method
• Editing a Data Handling Method
• Building a Recalculation List for Calibration
• Processing a Recalculation List to Add Calibration Data
• Reviewing Calibration Results
• Processing Analysis Files in a Recalculation List
• Reviewing Analysis Results
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Editing a Data Handling Method
Tutorial Topics
Qualitative Identification
Before you can build a calibration file and quantitate unknown samples, you must
analyze a standard sample at a known concentration level and identify the
compounds of interest. If you have not already done so, review the tutorial
“Qualitative Analysis of GC/MS Data”. If you have completed this tutorial, you
have already verified the identity of the nine analytes in the file 80_ng.sms.
Select the View /Edit Methods button to create a new data handling
method. In the Create/Open Method File dialog select Create a New Method
File and press OK.
Select Custom in the Select Configuration dialog.
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Select 2000 Mass Spec from the Configure Modules dialog, click the Add
button and then Next.
Check 2000 Mass Spec in the Detector Modules field and click Next.
Select Channel 1=MS Data, Standard MS Reports and MS Data Handling in

the Create sections for post-run processing dialog and then click Next.
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Tutorial Topics
To confirm configuration and post-run processes, click Finish in the next dialog.
Following these actions, the Method Builder dialog will open with a directory tree
on the left side showing an outline of the sections available for editing.
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As shown in the directory tree, the MS Data Handling method contains three
sections:
Calculations Setup - where you will set global parameters for calculation type
(Area/Height; Internal/External Std.) and for processing of unknown peaks in the
chromatogram
Compound Table - where you will identify internal standards, set calibration
concentration levels and adjust quantitation ions and other compound-specific
parameters
Results Treatment - where you will set additional rules for Calibration replicates,
and set rules for the treatment of failed peaks in Analysis and Verification
samples
As you explore the parameters in these data handling method sections,
remember that you can discard any edits you have made in a dialog by clicking
on the Restore button.
The Calculations Setup Dialog Box

Click on the Calculations Setup section. Set the parameters as shown next.
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The Calculations Setup Dialog Box
Explore the other features if you like, but use these defaults for this tutorial. The
upper General section now specifies to do measurements by Peak Area and
calibrate via an Internal Standard approach. Missing and Unknown peaks will be
reported. In the Chromatogram Processing section, observe that the
Reconstructed Ion Current (RIC) will be used for integrating unknown peaks and
they will be quantified by using the RF of the nearest internal standard.
Additionally, the Unknown peaks will be Library-searched using the tutorial.lbr
library. Any Unknowns identified by the library search will become Tentatively
Identified Compounds (TICs). In data handling Reports, results for TICs will
include their library search name and CAS Number (if these are present in the
library entry of the match spectrum). Finally, we have chosen to report only the
largest 20 Unknown peaks in the chromatogram. The Exclude Duplicates choice
prevents peaks which have been identified as Target Compounds from also
being reported as unknowns or TICs.
Select Library Search Unknown Peaks, click Search Parameters and use the
same parameters shown next:
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Press Save to return to the Calculations Setup dialog.
NOTE: Although we have briefly explained the chromatogram processing

parameters, this tutorial does not deal with processing unknown peaks. Refer to
the Software Reference Manual for an in-depth discussion.
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The Compound Table
The Results Treatment Dialog Box
Click on the Results Treatment dialog in the Method Directory. Explore the
options available in each section of the dialog. For this tutorial, use the values
shown for each field.
Note that rules have been set for tolerances and Out-of-Tolerance Actions for
Calibration, Analysis, and Verification samples.
The Compound Table

When you select the compound table from the directory tree, the compound table
dialog is opened as well as the Select Centroid MS Data File dialog to open the
file used to build the compound table. Select the file 80_ng_sms from the MS
Tutorials folder and click on the Open File button.
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The Data File Name field in the compound table dialog shows the file that is
being opened:
Click on the Build Compound List button to create a new compound list. This
action opens the MS Data Review application:
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The Compound Table
Select the Spectrum List >Build Spectrum List from Active Chromatogram
command.
The Edit Integration Parameters dialog is opened. By using the default values,
the list will include the compound Hexachlorobutadiene at a retention time of
about 8.233 minutes, besides the nine compounds that we use for quantitation in
this tutorial. The area of this peak is just below 1500 so, to have the software
ignore this peak set the Peak Size Reject (counts) parameter to 15000 and click
OK. Also, change the Slope Sensitivity(S/N) setting to 10 in order to find the
Benzoic Acid peak. Click OK to process the file.
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Select the Library Search Spectrum List button in the Spectrum List
window and use the Tutorial library for searching the spectrum list. In the NIST
Search for Target Spectrum dialog click the Edit/Order Library List tab.
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The Compound Table
If Tutorial library is not listed, click the Add Libraries tab. Select the Tutorial
Library from the list and click Select.
Select the other libraries listed in the NIST Library Manager dialog (in the
picture above they are MAINLIB and REPLIB) and click the Inactivate Library
tab. Press Done to close this dialog and then Search in the NIST Search for
Target Spectrum dialog. Save the search results by selecting the Update All
Searches with Matches button .
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Close the MS Data Review application. In the Method Builder dialog click on the
Import Compound List button. You will be prompted to a dialog for selecting the
spectrum list. The compound list has the name of the file it was created from (in
our case it is 80_ng.msp).
After you press the Select tab, the compound list is imported in the compound
table of the Method Builder dialog.
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The Compound Table
The compound table consists of eight columns with the following information:
Retention Time, Compound ID, Quantitation Ions, Calculations, Integration,
Identification, and Reference Spectrum. Double-clicking one of these tab dialog
fields for a compound will allow you to view and edit all of the information in the
dialog.
Compound ID Tab Dialog

Double-click in the Compound ID field for the compound Naphthalene-d8. You
will see the following dialog:
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As the display above shows, Naphthalene-d8 will be identified as an analyte;
click on Internal Standard instead. The CAS# for this compound is missing. Click
in the CAS Number field and enter 1146652 (without using any dashes as
separators - note that the dashes are entered automatically for you).
NOTE: In addition to typing in a value, you can change the retention time in this
dialog simply by clicking on the chromatogram at the desired time.
Now use the Next and Previous buttons to check the Compound ID information
for the other analytes. You will notice that Naphthalene-d8 is identified as the
Internal Standard to use for the other compounds. You may change to other tab
dialogs for the current compound by clicking their tabs in the top of the display.
Return to the main Compound Table window by clicking the Close button.
Quan Ions Tab Dialog

Double-click on the Quan Ions field for the compound 2,4-Dichlorophenol. When
peaks were added to the Compound Table in MultiChro, the Quantitation Ion
default was the Base Peak (most intense) ion in the mass spectrum for each
peak. Note that the plot shows the mass chromatogram for the chosen Quan Ion.
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The Compound Table
You may choose another quan ion, a sum of ions, or a range of ions for
quantitation by entering the information in the Quan Ions field. Click on the
combo box to display the options and click Ion(s).
The Select Ions to Plot dialog will open. To add two or more ions separate their
m/z values by a “+” sign. For example, you might want to add ions 63, 98, and
162 for quantifying 2,4-Dichlorophenol. To do this you would enter 63+98+162 in
the Quan Ions field. A range of quan ions from 162 to 164 would be entered as
162:164 in the Quan Ions field.
NOTE: The Scan Function Channels field is only relevant to MS/MS analysis, in
which quantitation may be done on individual Channels of information.
The default base peak Quan Ions are appropriate for quantitation of all of the
peaks in this Compound Table. You can use the Next and Previous buttons to
examine the Quan Ion information for other peaks in the Compound Table.
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NOTE: You can change the compound retention time in this dialog simply by
clicking on the chromatogram at the desired time.
In addition to specifying quantitation ions in this tab dialog, you may also select
qualifier ions. Click Load to automatically enter the three most intense qualifier
ion candidates.
Note that both the quantitation ions and the allowed qualifier ions must be
present in the Reference Spectrum. By clicking Add you can add the next most
intense reference spectrum ion available. To change a selected qualifier, click
the combo box in the Ion field to see the available choices. The Ratio field shows
the intensity of the qualifier ion as a percentage of the chosen Quan Ion(s). The
% Uncertainty field is the allowed percentage deviation from the Ratio. By default
this entry is 20%, but it can be adjusted. Therefore for the top Qualifier shown
here, the allowed range for the ratio of the peak area of the Qualifier Ion m/z 63
would be 87.5 ± 20% = 67.5 to 107.5% of the area of the Quantitation Ion m/z
162 if the Ion Ratio Type in the Calculations Setup is Absolute.( These values
would be 70.0-105.0 if it was Relative to the actual Ratio value). When samples
are processed as Calibration, Analysis, or Verification runs, the Qualifier Ion tests
will be run automatically.
Calculations Tab Dialog

Click on the Calculations tab from the current tab dialog. Use the Previous
button if necessary to move to the first compound in the list, 2,4-Dimethylphenol.
In the Calculations dialog we will enter information about the number of
calibration levels and their concentrations. We can enter this information for the
first compound in the table, then use the Fill Down feature to apply it to the other
analytes in the Compound Table. Although we will not be changing most of the
default options in the Calculations dialog for this tutorial, you may wish to explore
these options. For example, instead of a Linear Curve Fit calculation, Quadratic
and Cubic fits may be chosen. Also, the Origin Point may be the default Ignore
(do not include in data set), Include(add the origin to data set), or Force( force
curve through zero point).
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The Compound Table
For this tutorial, we will use calibration information at seven different levels. Enter
7 in the # Calibration Levels field. You will see the Cali Level Amounts field
change to allow entry of the different levels. Then, click in the first level in the
field Cali Level Amounts. Enter the following amounts for Levels 1 through 7: 10,
20, 40, 80, 120, 160, 200. Enter a Report Threshold of 1.000 and Results Units
of PPB. Note the Reports Threshold can be set on a per-compound basis. This
feature can be used to eliminate reporting of quantitation results for Analysis
samples below the Practical Quantitation Limit (PQL), which is generally defined
as 5-10 times the Method Detection Limit (MDL). The display should now appear
as shown here:
Click on the Close button. Now the Calculations Information for the first
compound is updated in the main Compound Editor dialog. You can fill this
information automatically for the other compounds in the table. Click the
Calculations Tab to highlight all entries, or select the desired block of field cells
by clicking and dragging with the mouse.
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Then click the Fill Down button. Now the concentrations of the seven
calibrations levels are filled in for all analytes. You need to make one further
modification to complete the editing process. The internal standard Naphthalene-
d8 is actually present at 40 ng/µL in all seven files. Double-click on the
Calculations tab for Naphthalene-d8 and change the Cali Amounts to 40 for
Level 1.
Finally, Click Copy Amounts to enter 40 automatically to the other levels.
Integration Tab Dialog

Click on the Integration tab field for 2,4-Dimethylphenol. The default integration
parameters for Peak Width, Slope Sensitivity, and Tangent % will provide good
integration data for peaks with good shapes and normal widths.
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The Compound Table
Check how the peak will be integrated by clicking the Integrate button. You will
see the baseline drawn in the Chromatogram display and the peak area and
retention time displayed to the lower left side of the Integration dialog. For this
compound the integration process works well with the default integration
parameters.
Integrating Difficult Peaks

Because no column phase will provide good peak shapes and resolution for all
analytes, you will need to adjust the integration parameters to get good
integration on some peaks.
Peak start and end points are detected by comparing the calculated slope at
each point to the slope threshold, and therefore are greatly affected by the Peak
Width and Slope Sensitivity parameters. The slope is calculated on a segment
centered around the point, whose size is derived from the Peak Width parameter
value. This means that increasing the Peak Width tends to move the peak start
and end points out from the peak apex. This increases the probability that broad
peaks will be detected, and tends to smooth out irregular or split peaks during
processing (the display is not affected). Typically, a Peak Width value slightly
larger than the actual peak width at ½ height works best. In contrast, changing
the Slope Sensitivity changes the slope threshold directly. This means that
decreasing the Slope Sensitivity also moves the start and end points out from the
apex, and increases the probability that small peaks will be detected. Because
these parameter have different effects, you may need to vary one or the other or
both to get the best results for a given peak. Increasing the Peak Width and/or
Slope Sensitivity for broad, poorly shaped, or split peaks often improves the
accuracy and reproducibility of integration results.
The benzoic acid peak is a good example for exploring the effects of the
individual parameters and their interactions. Click Next until the integration data
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for benzoic acid appears. Now click on the Integrate button to integrate the
benzoic acid peak.
Benzoic acid is integrated, but the segment end point is too high. Increase the
Peak Width parameter. You will discover that this parameter alone does not allow
good control for moving the ends of the segment defining the integration region.
When you increase the Peak Width up to 16 sec, both point ends are moved, but
they are too far out. Increase the Slope Sensitivity parameter from 20 to 160 and
integrate again.
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The Compound Table
You can have different integration parameters for different compounds in the list,
but for a given compound there is only one set of integration parameters for all
concentration levels.
After you find a good combination of integration parameters for the mid
concentration level data file, 80_ng.sms, confirm that they are acceptable at all
calibration levels by re-integrating the compound at several different
concentrations. It is particularly important to check the lowest and highest
concentration levels. To select a different data file, click Close to return to the
main table, then click Select Data File and select the desired data file, and then
return to the Integration page.
When you have finished adjusting the integration parameters for benzoic acid as
well as for the other compounds at different calibration levels, re-select the
80_ng.sms data file to continue with the tutorial.
Identification Tab Dialog

Double-click on the Identification field for 2,4-Dimethylphenol. Observe the
default parameters for peak identification. The default for Peak Window is ±
0.200 minutes (± 12 seconds). When the quantitation software is trying to find the
2,4-Dimethylphenol peak and integrate it, a spectrum matching the library fit
Match Threshold of 700/1000 must be found within this 24 second window
bracketing the expected retention time (found in the Compound Attributes
dialog). Ions in the Reference and Sample spectra below the designated
Minimum Abundence(%x10) value will be ignored in calculating the library fit. For
samples with significant matrix interferences, using Minimum Abundence(%x10)
values of 50-100 is useful in improving peak identification performance. The
integration must also occur entirely within this window. Therefore, always make
sure that the peak width is wide enough to allow a good integration to occur. The
default value will work fine for normal peaks without excessive tailing.
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You can use the default Identification parameters for all peaks in the Compound
Table except for benzoic acid. For this peak, enter a peak width of 0.400 min.
Reference Spectrum Dialog

Click on the Reference Spectrum tab for 2,4-Dimethylphenol. Observe the
Sample and Reference mass spectra. Note that the lowest intensity peaks in the
Sample spectrum are not included in the Reference spectrum. This is because
only the 16 largest peaks are included in the Reference spectrum. Notice that the
source data file for the reference spectrum is indicated in the File: field. Examine
the Ion/Intensity list. You may edit the reference spectrum if desired and redraw
the spectrum plot. Editing the reference spectrum is advisable if interference ions
(from coelution, background interferences, or column bleed) are observed in the
reference spectrum. If the spectrum is edited by the user, the File: field will be
changed to Manually Edited.
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The Compound Table
Use the Next and Previous buttons to scroll through the spectra for the analytes
in the Compound Table.
Checking Spectral Quality over the Calibration Range

Note that the Reference Spectrum dialog is a convenient place to examine the
quality of the mass spectra for the highest and lowest concentration levels of the
calibration curve. For example, you can examine the lowest and highest level
spectra for the analytes in this tutorial. Click Close for this dialog and select the
10_ng.sms using the Select Data File button. Look at the comparison of sample
to reference for each compound and verify that the reference spectrum (from the
80_ng.sms file first used to build the compound table) is a good match to the
spectra in the lowest level sample. The Reverse (R) Match (representing the
extent to which the reference spectrum is contained in the sample spectrum),
displayed below the Reference spectrum, should be higher than the Match
Threshold specified in the Identification dialog. Remember that the default
value of the Match Threshold is 700.
Next, use the Select Data File button in the Main Compound Table again to
compare spectra from the 200_ng.sms file to the reference spectra. This process
of comparison will assure that you have chosen good spectra for identification,
specifically ones that will perform well over the entire calibration range. You also
can check to see whether a different data file scan would generate a better
reference spectrum. When you click on a point in the chromatogram display, the
spectrum for that point is shown in the spectrum display. Click on the Put
Sample in Reference button to generate a new reference spectrum. When you
have finished comparing spectra, click on Close to return to the main Compound
Table dialog.
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NOTE: You may take this comparison process one step further by choosing for
comparison a data file for an analysis sample (e.g. a spiked matrix extract
sample).
Save the Edited Data Handling Method

Click on File >Save As.. to save the edited Data Handling method and type a file
name in the Save Method File As dialog (in our case, the method is named
calibration.mth). Click on File >Exit to close the Method Builder.
You have now finished building and editing a data handling method for the 2000
GCMS Workstation. The next step in the quantitation process is to build a
Sample List or Recalc List to add calibration points to the Data Handling method.
Building a Recalculation List for Calibration

A recalculation list contains all the data files used for calibrating the quantitation
(determining the calibration curve) and for analysis. The recalculation list is built
in the Automation File Editor that can be accessed in different ways:
1. Click on the Automation File Editor application button from the

Varian Workstation toolbar.
2. Right click on a data file name (in the Data File Pane of the MS Data Review
window) and select Recalc List File >Edit.
3. Click on the Process Data button in the MS Data Review toolbar to

open the Process Data view
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Building a Recalculation List for Calibration
The Compound Table
Click the Edit tab in the Recalc List File field.

All these three actions will open the Automation File Editor dialog, where you
will build now a new recalculation list.
In the Automation File Editor select the menu command File >New
>RecalcList
Type a file name and choose a directory where you want to save the
recalculation list and press Save in the Create a new RecalcList File dialog.
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An empty Recalculation List is opened in the Automation File Editor. You will
now enter the file names for the data files at each concentration level and
associate them with the Calibration Levels identified in the Calculations tab
dialog in the Compound Table editor (see the previous section of the tutorial
under (Calculations Tab Dialog). For your convenience the calculation levels
entered in that dialog are copied here:
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Processing a Recalculation List to Add Calibration Data
The Compound Table
Position the cursor in the Data File field of Row 1. Click and then
click . The Open Data File dialog will appear. Select the data file
10_ng.sms in the directory C:\VarianWS\MSTutorials. In the Sample Type field
use the pull down arrow and choose Calibration. Then click in the Cal. Level field
and enter 1. (Note in the figure above that Calibration Level Amounts 1 is
identified as the 10.000 level.)
Use the same procedure to enter the data file 20_ng.sms. Select Calibration in
the Sample Type field and enter 2 in the Cal. Level field. Continue to add lines for
the 40, 80, 120, 160, and 200 ng level files until all seven levels are entered to
the Recalculation List quantitation.rcl. To assure that calibration data are cleared
before calculations, highlight the first Row of the list and click and
select New Calibration Block in the Sample List field. When you are finished,
the recalculation list should look like the following:
Use the menu command File >Save to save the Recalc List. Click on File >Exit
to close the Automation File Editor.
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Open the Process Data view in the MS Data Review application by clicking the
“Process Data” icon . If you opened the Automation File Editor from the
Process Data view (as described in action 3 in the previous tutorial), you will
return automatically here when you close the Automation File Editor after
saving the recalculation list. The data handling method file should be
calibration.mth. Click the Recent button in the Recalc List File field and select
quantitation.rcl.
Select All Lines in the Processing Rules field.
Click on . As the Data File list is processed, a message log and a

process indicator at the bottom of the display keeps you advised of the progress.
The current line in the list is shown followed by the word Processing, until the last
line has been completed.
Examining Calibration Results in Process Data View

You can view and print calibration reports in the Process Data View. Check
Preview Reports in the File menu of the MS Data Review window.
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You can view calibration block and curve reports as well as summary and chart
reports by clicking the Print button in the Process Data view and making the
report selection. If the Preview Reports option is not checked in the File menu,
any print command will send the report file directly to the printer, without opening
a preview window. Press Print and Select Calibration Curve Report
This will bring up a Print Preview screen for the calibration results. Four
calibration curves are shown on each page. Use the Next/Previous Page
buttons to examine other curves. You can click and drag in the display
to expand the screen for better viewing, or you can click the Print Page or Print
Report buttons to send it to your printer.
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Reviewing Calibration Results in the Results View
Open the View Results window by clicking the Results button in the MS
Data Review toolbar.
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In the Results view you can examine the calibration and analysis results and
interactively adjust the integration parameters for any compound in any data file,
which you select from the list displayed on top of the Results view.
You can manually integrate peaks in the Integration pane by manually moving
individual peak event markers. Place the cursor on a peak event(the cursor will
change to a hand symbol), then click and drag to the new location.
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After releasing the mouse drag the peak will be reintegrated and the moved peak
event will be shown filled in with the old position still showing, but marked with an
“X”. To restore the original peak event position, right-click on the event and
select to restore event. The peak will be reintegrated again to the original results.
Alternatively, click on the Set Click and Drag Action button in the
Integration pane toolbar and select Integrate Area.
Select the integration region by clicking and dragging along the base of the peak
(the newly integrated region will appear red).
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NOTE: This example showed a change made to a calibration data file. This will
cause all the calibration data files to be reintegrated to generate a new calibration
curve and, in addition, any analysis data files will be reintegrated to generate
updated results. If a change is made to an analysis data file, then only that data
file will be reintegrated.
You can also modify the integration parameters entered in the data handling
method by clicking the Edit tab in the lower left side of the Results view.
This action will open the Integration field in the compound table for the compound
selected in the Results view.
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You can change other parameters besides the integration parameters for this
compound (in the Identification, Calculations, Ref. Spectrum or Quan Ions fields),
but you cannot select another compound in this dialog.
When you make parameter adjustments, the results are automatically updated in
the Results view.
NOTE: All changes to the method and data file results in the Results View
window are stored to temporary files. These changes will only be saved to the
actual files when exiting the Results View window or by clicking on the Save
button or by loading a new recalclist or a new data file. You will be prompted to
save the changes, delete the changes or cancel the save operation.
Examine the calibration results by selecting the compounds and data files in the
list. The Amount field in the upper pane displays two types of information,
depending on whether it describes a calibration file or an analysis file (the file
type information was entered in the Sample Type field of the RecalcList dialog in
the Automation File Editor):
For calibration files, the Amount field contains the Relative Response Factor,
RRF, defined as:
RRF=(Peak Area/Peak AreaIS) x (AmountIS/Amount)
Area will be replaced by Height in this formula, if height is the selection in the
Measurement Type field of the Calculations Setup section in the Data
Handling Method (see the section Editing a Data Handling Method presented
earlier in the tutorial).
For the analysis files, The Amount field contains the quantitative amount. Note
that for the Internal Standard, Naphthalene-d8, the Amount value is 1 for the
calibration files.
You can view and print reports from the Results view by pressing the Print
button in the left lower side of the View Results dialog and selecting the type of
report.
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Viewing and Editing Calibration Results in the Method Builder Dialog
Again, make sure that the Preview Printed Reports is checked in the File menu
of the MS Data Review window.
Viewing and Editing Calibration Results in the Method

Builder Dialog
You can also view the calibration curves from the Method Builder window. Open
the method created and used in this tutorial on quantitation, in our case the
method file name is calibration.mth, either by clicking on the View/Edit Methods
button in the Workstation toolbar, or by using the quick link button.
Click in the Compound Table section of the Method Directory under MS Data
Handling. The Compound Table dialog appears.
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Click on the View Curves button. The calibration curve for the currently selected
compound in the Compound Table is displayed.
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Processing Analysis Files in a RecalcList
Viewing and Editing Calibration Results in the Method Builder Dialog
Notice that the Curve Fit options chosen when the Compound Table was built are
defaults for the display (Linear Fit, Ignore Origin Point). The linear fit equation for
2,4-Dimethylphenol is shown above the plot field. Click on the other Origin
options, Include Origin Point and Force curve through the origin. Observe the
change in the fit equation and the Correlation Coefficient. Now try Quadratic and
Cubic curve fits and observe the fit equations and correlation coefficients that
result. Note that for most well behaved species analyzed by GC/MS the Linear fit
and ignoring the origin point provides the simplest route to good quantitation
results.
Click on the up/down arrows in the Peak Name field to observe the curves for the
other compounds in the Compound Table. If you have changed the fit options
you will be asked whether you wish to keep the edits.
Double-click on one of the data points of the calibration curve graph, for example
the 80 ng level for 2,4-Dimethylphenol. Observe the new Point Info dialog
appearing below the Calibration Curve dialog.
As you can see in the Calibration Curve plot, this data point has a greater
deviation from the fitted line than other data points for the compound. Note the
deviation value of –4.52% in the Point Info dialog. Click on the box Exclude
Selected Point from Calculation. Observe the change in the fit equation,
response factor RSD, and the Correlation Coefficient when the point is excluded.
Points may also be excluded from the calculations by right-clicking on the
selected data points in the plot. This is a toggle function. Right-clicking on an
excluded point will include it again.
NOTE: The process of excluding data points does not remove the data points
from the Compound Table. However, exclusion does affect the calibration
calculation and the quantitation results.

Processing of analysis files is performed in the Process Data view. There are
two ways to process files as Analysis Samples. You can add files to the existing
RecalcList used for calibration, or you can just process the currently active file
opened in the chromatogram display. Both ways will be exemplified in the
following.
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Adding and Processing Entries in an Existing
RecalcList
You have learned how to process a Calibration Block using a Data Handling
method and a RecalcList. Now it is time to process Analysis files in a RecalcList.
Open the Process Data view. If they are not already selected, choose the files
calibration.mth and quantitation.rcl for the active data handling method and
RecalcList, respectively.
In the RecalcList File line, click Edit to enter the Automation File Editor. Click
Add to add a new entry, which will have a default Sample Type of Analysis.
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Adding and Processing Entries in an Existing RecalcList
Click Browse to select a file for analysis processing and select the file
50ng_ccc.sms.
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Click Open to close the file selection dialog and enter this file name for the
Analysis entry in the RecalcList.
If you have already processed the Calibration files, you could delete the New
Calibration Block entry and the seven Calibration files before Processing the
RecalcList but this is not necessary. Save the RecalcList and close the
Automation File Editor. You can now perform the Recalculation immediately by
selecting All Lines and clicking the Process button. You will be able to observe
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the progress of the recalculation in the processing status field below the Data File
Table. At the end of the run the screen will look like this.
To only process the 50ng_ccc.sms file, you can select Selected Lines, highlight
the 50ng_ccc.sms line and then click Process (make sure that Clear Calibration
is not checked).
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Processing the Active Data File
Alternatively, open the chromatogram to be analyzed by selecting the data file
name in the Data File pane of the Plot Chromatograms and Spectra view.
Select the same analysis file, 50ng_ccc.sms, as in the previous tutorial.
Select the Process Data button in the MS Data Review toolbar. This will
open the Process Data view, which has in the Method File field the last method
file used (usually to run the Calibration Block) and in the RecalcList File field a
new recalclist file (named by default ActiveFile.rcl) that contains the currently-
active data file.
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When a calibration is processed, the calibration information including the

calibration files that are used, are added to the Calibration Block of the data
handling method used for processing. Since you performed the calibration in the
previous tutorial, all this information is contained in the method file
calibration.mth. To run the analysis, all you have to do is click the Process
button (make sure that Clear Calibration is not checked). As before, the
processing status display field will show when the processing is complete.
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Reviewing Analysis Results
The results for the analysis files you have just processed can be reviewed in the
same way as calibration results, from the Process Data view or the Results
view.
In the Process Data view, click the Print tab, and select among the listed
options. Verify that Preview Printed Reports is checked in the File menu of the
MS Data Review window, as mentioned in the previous tutorials.
Previews of the selected reports will be opened, which you can examine page-
by-page and/or print, as previously described for reviewing the calibration results.
Open the View Results dialog by clicking the View Results toolbar button .
As only the analysis file was processed, the list displayed on top of the Results
view contains only the compounds of this data file.
For the Analysis sample type, the Amount field reports the quantitative amounts
of the compounds, instead of Relative Response Factors that are reported for the
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Reviewing Analysis Results
Calibration files. This data file has all of the Target Compounds present at 50 ng
levels. All but the Benzoic Acid peak show good quantitative results. Adjusting
the integration and curve fit parameters for the benzoic acid species would
improve results for this compound. These operations can be performed in the
Integration pane of the Results view and in the Method Builder dialog as
previously described for adjusting parameters to improve calibration results).
One compound, Hexachlorobutadiene, was also tentatively identified during
Chromatogram Processing of unknown peaks. This TIC unknown has a different
retention time and lower spectrum match than the compound identified as
Hexachlorobutadiene. This suggests that it is in fact a structurally similar, but
different compound.
Remember that the parameters for processing unknown peaks are set up in the
Calculations Setup dialog of the MS Method in the Method Builder application.
It can also be accessed from this screen via the Edit button.
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SIS and MS/MS Acquisitions
Introduction Tutorial
Calibration of SIS
Using the Selected Ion Storage (SIS) option, you may selectively accumulate or
store specific ions in the trap. The ejection of the unwanted ions is performed by
applying a multifrequency waveform, which includes those frequencies required
to eject the unwanted ions and misses the frequencies corresponding to the
stored ions. The waveform amplitude will be adjusted so that there is good
ejection of matrix ions while the desired ions are still stored efficiently.
This tutorial assumes that you have a basic knowledge of 2000 GC/MS operation
and that your instrument has been tuned.
To perform SIS calibration, you will first build a SIS Method to isolate three ions,
m/z=100, 264 and 414 from the calibration gas spectrum. Open the Method
Builder application from the Workstation Toolbar. Open a GC/MS method and
edit the MS section. Create a two-segment method as shown below.
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The first segment detects all ions in the calibration gas in the mass range of 60-
650 in the EI Auto mode (no ion preparation). The second segment selectively
stores the m/z 100, 264 and 414. To set up the Storage Mass Range for SIS
highlight the second segment in the segment table (as shown above), then select
the Ion Preparation - SIS tab dialog. Under the Storage Mass Ranges enter the
values shown in the picture. Click the Customize button and make sure that the
Autoscale field is checked.
This selection will assure that optimum waveform amplitude is calculated, which
will eject all the ions except the ones selected for storage. You can further
optimize the waveform amplitude value by adjusting the SIS Amplitude Adjust
Factor in the Auto Tune mode in System Control as will be described later in
this tutorial. Save the method file as CalSIS by using the menu command File>
Save As and then close the Method Builder application.
Select the System Control application from the Workstation Toolbar. Use the
menu command File >Activate Method. From the selection dialog select
CalSIS.mth and click Open. Select the Manual Control mode in System
Control. Turn on the trap and the calibration gas by clicking the ON/OFF and Cal
Gas symbols in the schematic picture in the Control and Status field (see
picture below). The color of the symbols will turn green showing which
components of the instrument are turned on. Use the Segment # field in the
Method display to select the desired segments.
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Calibration of SIS
The mass spectrum displayed in the above picture was acquired with segment 1.
It shows all ions in the calibration gas, as there is no ion preparation selected.
Select the second segment that uses the SIS ion preparation to store only the
m/z 100, 264 and 414. The mass spectrum acquired with segment 2 (SIS on)
shows only the selected ions.
A SIS calibration determines the minimum waveform amplitude so that unwanted

ions are efficiently eliminated while the peak intensities of the selected ions are
maximized. This calibration is performed by finding the lowest SIS Amplitude
Adjust Factor. This factor represents the percentage of the waveform amplitude,
which was automatically determined by checking the Autoscale field in the
Customize SIS Method dialog, as mentioned previously. The spectrum shown
above (SIS on) was acquired with the default value of 100 for the SIS Amplitude
Adjust Factor. Note the base peak intensity using the scan display.
Click on Auto Tune and select the Set Points tab.
Set the SIS Amplitude Adjust Factor to 50 (the values may be set between 50
and 200) and acquire another spectrum with segment 2.
The waveform amplitude value is too low (50% of the one calculated by choosing
Autoscale) and as a result the unwanted ions are not ejected effectively. Note
that the base peak ion is 131 and the its intensity is lower compared with the
base peak intensity in the first spectrum due to the fact that EI Auto sets an
optimum limit in the total number of ions stored in the trap.
Set now the SIS Amplitude Adjust Factor to 90.
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The base peak ion is 264 and its intensity increased, however the ejection of the
131 ion is not complete.
For this ion trap system, a SIS Amplitude Adjust Factor of 100 gives the most
effective ejection of undesired ions while providing optimum base peak intensity.
MS/MS
1. Isolating m/z 265 From Cal Gas
In this tutorial you will build an MS/MS ion preparation method that isolates m/z
265 in the cal gas spectrum. Isolating a small peak (m/z 265) in the presence of a
large peak (m/z 264) will assist you in learning how to optimize isolation
parameters and how the parameters affect the spectrum. The constant source of
ions from cal gas facilitates learning how to adjust the MS/MS parameters.
This tutorial represents the first part of a MS/MS method, which is the isolation of
the parent ion. To acquire a mass spectrum of the parent ion, we need to set the
dissociation amplitude to zero, which means that no fragments are created and
only the parent ion is detected.
Open the View/Edit Method application from the Workstation Toolbar and
build a MS/MS method by using the parameters shown next. In the Parent Ion
Mass field type 265 and choose an isolation window of 2. Set the Excitation
Amplitude to zero in the Dissociation Field.
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MS/MS
Save the method by using the command File >Save As in the Method Builder
menu and type a file name in the Save Method File As dialog. Close the
View/Edit Method application and open the System Control application.
Activate the method you just built by using the command File >Activate Method.
Turn on the calibration gas and the trap. Observe the spectrum. If any of the
peaks are off scale (> 4088 counts), reduce the AGC Target TIC Value in the
method. (This can be done quickly by clicking on the Method button and making
the change. When you close the Method Builder dialog you are asked if you
want to save the changes and reactivate the method. Click Yes in both dialogs.)
If the mass spectrum contains both m/z 264 and 265, the isolation window is too
large.
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In the method, lower the Mass Isolation Window value to 1.
Return to System Control and acquire a mass spectrum with these changes. The
264 peak might still be present but its size should be reduced. To further optimize
the isolation of m/z 265 from the m/z 264, you can do the following. In the
method, click on segment 2 in the list. Click on the Ion Preparation-MS/MS tab
and then select the Customize button.
The Low Edge Offset parameter in the Isolation field affects the isolation window
on the low mass side of the parent ion. Decreasing the offset (the default value is
6) decreases the window on the low mass side. Set the Low Edge Offset to 4 and
close the dialog by pressing OK. Keep the Isolation Window value to 1, return to
System Control and acquire a mass spectrum with these changes.
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MS/MS
Observe that the m/z 264 peak is further reduced considerably. Now decrease
the Low Edge Offset value to 2 and acquire a mass spectrum.
The m/z 265 ion has been isolated but its peak intensity has also been slightly
reduced due to the fact that the isolation window has become too narrow by
decreasing the Low Edge Offset value to 2.
2. CID of M/Z 264 from Cal Gas Using Nonresonant Excitation

In this tutorial you will build a MS/MS method for the m/z 264 ion in the
calibration gas using nonresonant excitation. You will optimize the excitation
amplitude to achieve a good distribution of product ions. This optimization is
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performed by acquiring mass spectra with different values of the excitation
amplitude.
This tutorial assumes that the trap temperature has been set to 150 °C. Other
trap temperatures may require adjustment of the excitation voltages. Open the
Method Builder application and build a MS/MS method by using the parameters
specified below.
Set the Parent Ion Mass to 264 and select an Isolation Window of 2. The mass
range for the MS/MS segment is 50-350. In the Dissociation field set the
Waveform Type Non-resonant, the Excitation Storage Level to 65 and the
Excitation Amplitude to 30. Click the Customize tab and set all the parameters to
their default values. In the Segment Setpoint field set the Emission Current to
20 μA. In the Ionization Mode - EI Auto, set the Target TIC value to 10000.
Save the method and close the Method Builder application. In System Control
activate the method and turn on the calibration gas and the trap.
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MS/MS
If the m/z 264 is the only ion in the mass spectrum, a higher voltage is needed to
dissociate m/z 264. Click the Method button, increase the Excitation Amplitude
to 40, save the changes and reactivate the method. Turn on the trap and the
calibration gas and observe the spectrum.
The m/z 264 peak is still large, the Excitation Amplitude can be increased more.
Set the Excitation amplitude to 50 and repeat the steps described above to
acquire the mass spectrum.
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The parent ion m/z 264 is totally absent. You may choose an intermediate value
of 45 for the Excitation Amplitude. If the m/z 264 peak is small and the product
ions are visible (m/z 214, 176, 164, 154, 114), the voltage will be a good one to
use. Set the Excitation Amplitude value to 45 and record the mass spectrum.
3. CID of m/z 264 from Cal Gas Using Resonant Excitation

In this tutorial you will build a MS/MS method for the m/z 264 ion of the cal gas
using resonant excitation. As in the previous tutorial, you will optimize the
Excitation Amplitude to achieve a good distribution of product ions.
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MS/MS
This tutorial assumes that you have set the trap temperature to 150 °C. Other
trap temperatures may require adjusting the excitation voltages. Open the
Method Builder and build a MS/MS method by using the parameters specified
below:
In the Dissociation field, set the Waveform Type to Resonant, the Excitation
Storage Level to 50 and the Excitation Amplitude to 0.1 Click the Customize tab
and set all the parameters to their default values. Set the Emission Current to
20 μA and the Target TIC to 10000, as in the previous tutorial.
Save the method and close the Method Builder application. In System Control
activate the method and turn on the calibration gas and the trap.
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If m/z 264 is the only ion present in the mass spectrum, a higher voltage will be
needed to cause collision-induced dissociation of m/z 264. Set the Excitation
Amplitude value to 0.3 and acquire the mass spectrum as described previously.
The height of the m/z 264 peak should be reduced and several product ions
should be visible: m/z 214, 176, 164, 154, 114. The voltage may be further
increased to convert additional parent ions into product ions. Set the Excitation
Amplitude value to 0.5 and record the mass spectrum.
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MS/MS
If the m/z 264 peak is small and the product ions are visible: m/z 214, 176, 164,
154, 114, the voltage will be a good one to use. For this ion trap system, the
optimum value of the Excitation Amplitude is 0.5.
Further increase the Excitation Amplitude to 0.6 and observe the spectrum.
If the m/z 264 peak is absent and only the product ions are visible (m/z 214, 176,
164, 154, 114) with smaller peaks than before, the excitation voltage is too high.
If only the m/z 264 peak remains, try increasing the modulation range in the
Customize dialog.
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The product ion distribution using resonant excitation is slightly different from the
one obtained with nonresonant excitation.
4. Determining the Optimum Excitation Amplitude and

Excitation Storage Level for Nonresonant Excitation Using
Automated Methods Development (AMD)
In the previous two tutorials we showed how we could optimize the Excitation
Amplitude manually, by entering different values and recording the mass
spectra corresponding to each value. This procedure can by automated by
selecting the Automated Methods Development (AMD) option under the Ion
Preparation field in the Method Builder dialog.
AMD can be used to automatically optimize both the Excitation Storage Level
and the Excitation Amplitude. Follow these steps to optimize the nonresonant
excitation by using AMD while using the constant source of ions provided by the
calibration gas.
Open the method builder and build a method with the parameters shown below:
1. For segment 2, select AMD in the Ion Preparation field and set the scan
range 50-350. Click the Ion Preparation - AMD tab and set the Parent Ion
Mass to 264, the Isolation Window to 2 and the Waveform Type Non-
resonant.
2. The Excitation Storage Level depends on the lowest product ion mass, which
in our case is m/z 114. Set the excitation storage level equal to the lowest
product ion mass expected divided by 1.4. If the product ions are not yet
known, start with the excitation storage level of m/z 48 and an excitation time
of 20 ms. In our case a good starting excitation storage level is m/z 80.
3. In the Excitation Amplitude field, enter the first value 0 and then, starting with
20, increment each value by 10. There are a total of 10 entries for the
Excitation Amplitude values.
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MS/MS
4. Save the method and close the method builder. In System Control, activate
the method and turn on the trap and the cal gas. Observe the spectrum
corresponding to each value of the Excitation Amplitude. If any of the peaks
are off scale (> 4088 counts), reduce the Target TIC in the Ionization Mode
— EI Auto field. You might need to change the range of variation of the
Excitation Amplitude and/or to vary its value by smaller increments for a
more accurate optimization. While the spectrum is updated, observe the
channel number so that you can identify the excitation amplitude for the
optimum distribution of product ions.
For a more accurate optimization you might want to save the data by acquiring
the mass spectra in the Acquisition mode. You can then record the peak
amplitudes of the parent and product ions for each value of the excitation
amplitude and excitation storage level. To determine the optimum excitation
amplitude, you can use a different graphics program to plot the peak intensities
for the parent and product ions vs. the Excitation Amplitude. An example is given
below:
Nonresonant Excitation of a Typical Ion
1200
1000 Parent ion

Ion counts
800 Product ion 1
600 Product ion 2
400
200
0
0 10 20 30 40 50 60 70 80 90 100
Excitation amplitude (volts)
To optimize the excitation storage level, increase its value and repeat the cycle
through the excitation amplitudes as described above.
You can determine the optimum excitation storage level by observing the spectra
in Manual Control. As before, a more accurate optimization can be obtained by
saving the data after acquiring it in the Acquisition mode. You can determine
the optimum excitation storage level by plotting the product ion intensity as a
function of excitation amplitude for different storage levels. An example is shown
next.
Product Ion Formation vs. Excitation RF for a Typical Ion

Using Nonresonant Excitation
1000 RF=48 m/z RF=63 m/z RF=95 m/z

900
Product ion counts
800
700
600
500
400
300
200
100
0
0 10 20 30 40 50 60 70 80 90 100
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The maximum production of product ions shifts to higher CID (excitation)
amplitudes as the excitation storage level is increased.
5. Determining the Optimum Voltage for Resonant Excitation

Using Automated Methods Development (AMD)
Follow these steps to determine the optimum voltage for resonant excitation
using AMD while using the constant source of ions from the calibration gas.
Open the method builder and build a method using the parameters shown below:
1. Set the Parent Ion Mass equal to 264, the Isolation Window to 2 and the
Waveform Type Resonant. Set the Excitation Storage Level equal to the
lowest mass product ion expected divided by 1.4. We expect the lowest
product ion mass to be 114, so that a good start for the excitation storage
level is m/z 80. If the product ions are not yet known, start with the excitation
storage level of m/z 48 and an excitation time of 20 ms.
2. In the Excitation Amplitude field enter the first value 0 and then, starting with
0.1, increment each value by 0.1. There are 10 entries for the Excitation
Amplitude value. Note that much lower amplitude values are needed for
resonant excitation compared with nonresonant excitation. This is expected
since the transfer of energy is to the parent ion is much more efficient in the
resonant case vs. the nonresonant one.
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MS/MS
3. Save the method and close the method editor. In System Control, activate
the method and turn on the trap and the cal gas. Observe the spectrum
corresponding to each value of the Excitation Amplitude. If any of the peaks
are off scale (> 4088 counts), reduce the Target TIC in the Ionization Mode -
EI Auto field. You might need to change the range of variation of the
Excitation Amplitude and/or to vary its value by smaller increments for a
more accurate optimization. While the spectrum is updated, observe the
channel number so that you can identify the excitation amplitude for the
optimum distribution of product ions.
4. As mentioned in the previous tutorial, for a more accurate optimization of CID
excitation, you might need to record the peak intensities of the parent and
product ions and plot them as a function of Excitation Amplitude. For this,
you need to save the data from Acquisition mode.
You can plot the peak intensities of the parent and product ions as a function of
Excitation Amplitude by using a different graphics software. An example is shown
below.
Resonant Excitation of a Typical Ion
1200
1000
Parent ion
800
Product ion 1
600
Product ion 2
400
I
200
0
0 1 2 3 4 5 6 7
Increase the Excitation Storage Level by increments of 10 m/z and repeat the
cycle through the Excitation Amplitudes as described above. Acquire the mass
spectra in Manual Control and determine the excitation storage and amplitude
values for the optimum distribution of product ions.
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Run File Tutorials
Overview of the Varian MS Workstation for GC Run Files

The Varian MS Workstation contains 5 Star Workstation applications, which are
used to generate, process, and review GC run files. These files are produced by
standard GC detectors other than the 2000 MS. The Method Builder and System
Control/Automation (Chemis32.exe) applications are used for mass spec data
files as well, and are loaded automatically as part of the core Varian MS
Workstation software installation. The Report (Report32.exe), Batch Report
(Batchr32.exe), and Interactive Graphics/Data Handling (Ngig.exe) applications
are loaded if the Chrom Data Handling and Chrom Data Files/Methods options
are selected during installation. Each of these applications is represented by an
icon in the Varian MS Workstation program folder, as well as by a button on the
Star Toolbar (Starbar.exe).
Using the Star Toolbar

The Workstation Toolbar is designed to be a convenient starting place for all of
your interactions with the Varian MS Workstation. When you install the MS
Workstation, you can select to have the Workstation Toolbar displayed for you
automatically, whenever you start Windows. By simply clicking on a Workstation
Toolbar button you can invoke its associated application.
If the Star Toolbar is not present, open it by using the mouse to click on
Start >Programs >MS Workstation >Workstation Toolbar. Hold the mouse
cursor over each of the buttons in the Workstation Toolbar so that you can read
the tool-tip descriptions. You can find more options and complete descriptions in
the Help on Star Toolbar accessed by right-clicking in the free area on the right
side of the Workstation Toolbar.
Clicking on one of the buttons on the Star Toolbar will start or ‘launch’ the
corresponding application.
The applications that compose the Varian MS Workstation also allow a certain
amount of interaction. System Control can be used to start Method Builder and it
uses elements of the Report application when generating results and printing
them. From Report you can invoke Interactive Graphics and re-integrate the
chromatograms before printing them.
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Using the Tutorials
These tutorials are intended for demonstrating the data handling capabilities of
the Varian MS Workstation by having the user follow a set of step-by-step
procedures. Each procedure is followed by a picture to verify that the user has
performed the actions correctly.
After running the tutorials the user should have a good idea of how to use the
Workstation to reprocess chromatography data after it is collected.
Example Files
When you install the Varian MS Workstation software the ChromExamples
directory will be created in the directory where your workstation software is
installed. The ChromExamples directory contains files, which can be used for
learning about the Varian MS Workstation data handling capabilities. These
include calibrated Methods, a Sequence, a RecalcList, and data files. These files
can be used for comparison and to see various components of the system, such
as calibration curves, without having to build them yourself.
Reinstalling the Tutorial Files

If the tutorials have been run previously, you may wish to reinstall them so that
you can follow the specific instructions of the tutorials. To do this,
1. Insert Varian MS Workstation CD-ROM into the CD-ROM drive.
2. Select Install to start the Setup Program.
3. Select Update Ver. 6x to Ver. 6.5 MSWS. The installation dialog will walk you
through the next steps.
4. When the Product Serial Number dialog is opened, you don’t need to enter
the serial numbers (the existing products are highlighted).
5. Accept the Software License Agreement to continue.
6. Select the MS Modules.
7. When prompted from the Other Selections dialog, choose to install “Chrom
Example Data Files/Methods” and “Chrom Data Handling”.
8. Follow the next steps in the installation process and click Finish in the last
dialog. You will be prompted to dialog asking to Restart your Computer. Click
Yes.
The tutorials are arranged in a series that will help you utilize the data handling
capabilities of the Varian MS Workstation. Upon completing these tutorials, you
should be familiar with how to recalculate, reintegrate and calibrate data
collected with the Varian MS Workstation.
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Tutorial 1 Recalculating Results
Overview
The Varian MS Workstation allows you to recalculate results acquired with
standard GC detectors in Interactive Graphics and in System Control. Both
applications offer unique advantages for reprocessing data files. Interactive
Graphics lets you see the changes to the chromatogram in an interactive
environment. System Control lets you easily recalculate large groups of data
files as part of a sequence.
• Topics Discussed
• Reintegration with Moved Start/Ends
• Reintegrating
• Method Editing
• Recalculating in System Control
Preparing a Data File for Use with this Tutorial

Because PRACTICE.RUN is used for several tutorials, you should copy this data
file to RECALC.RUN for use with this tutorial.
In Windows Explorer.
View the C:\VarianWS\ChromExamples directory.
Use the right mouse button to click on PRACTICE.RUN, and select Copy.
Select Edit >Paste. A copy of this file is added at the end of the list.
Use the right mouse button to click on the new file. Select Rename, and type
RECALC.RUN.
Opening a Data File and Method in Interactive Graphics

Opening the Interactive Graphics application by selecting the Review
Chromatograms button in the Workstation toolbar.
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The Open Multiple Data Files dialog box appears.
Select the data file Recalc.RUN in the ChromExamples directory, and click the
Open File(s) tab.
Select File >Open Method... . The Open Method dialog box appears.
Find and select the method called ANOTHER.MTH in the ChromExamples
directory.
Integrate the peaks by selecting the menu command Results >Reintegration
List…
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The Reintegration List dialog opens. A check mark appears in the Run DH
column for the data file. This indicates that the file is selected for recalculation.
Click the Calculate Results tab.

To open the results file click on the chromatogram trace with the right mouse
button. Select View Results Only as seen in the menu below.
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The results for the data file appear. Note the areas for the peaks at 3.392 and
3.471 minutes. The results should appear as shown below.
Close the Results window by clicking on the in the upper right corner of the
window.
In Interactive Graphics, select View >Preferences. Select the TRACE
SETTINGS TAB. Click on the Radio Button called SHOW ALL EVENTS under
SHOW / HIDE PEAK EVENTS section.
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In the View menu of Interactive Graphics window check Locator Window and
Chromatogram Toolbar.
Now, zoom in on the center of the fused peak eluting at about 3.4 minutes. To
zoom, highlight the desired area in the locator window or highlight the region in
the main window from 2.5 to 4.0. (Areas of the display can be highlighted by
clicking on the upper left hand corner of the region you wish to zoom with the left
mouse button, dragging the mouse to the lower right hand corner of the area you
wish to display, and releasing the mouse button.)
Your display should look as follows:
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This enlarges the valley area between these overlapped peaks.
Moving a Peak Event

In the Interactive Graphics/Data Handling application, you have the ability to
move peak events manually. With this technique, you can accurately define the
placement of baseline peak events in instances where the automatic placement
of events was not optimum. You move a baseline event by clicking and dragging
the event triangle to a new location.
When you are adjusting the position of a start or end point, you may find it more
convenient and accurate to display the actual data points from the file on the
screen.
To hide the locator window:
1. Uncheck the Locator Window in the View menu and select the command
Preferences. Click on the Trace Settings tab.
2. Click on the Point option button under Plot Type. Click OK. The
chromatogram is now drawn as a series of dots representing the individual
data points from the file.
3. Place the cursor over the valley point between the two peaks.
4. Click the left mouse button, hold it down, and drag the valley point slightly to
the left.
When the cursor is at the new valley point location, release the mouse button to
move the valley point there.
Your window should look similar to this:
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Recalculating the Data File
Note that the peak event triangle for the valley point is now drawn as a solid
triangle indicating a moved peak event. Now that the point is repositioned, you
can recalculate the file using the moved baseline event.
Recalculating the Data File

After moving the valley point to a new position as described in the previous
section, reintegrate the peaks by using the command Results >Reintegration
List… and clicking the Calculate Results tab.
Open the results by right-clicking on the chromatogram trace and selecting View
Results Only.
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The areas for the peaks at 3.391 and 3.470 minutes have changed as a result of
the change in the valley point between them.
You can also move the peak start and end points and then reintegrate the peaks.
The Workstation uses the new points in the peak-processing algorithm.
You can return the valley point and/or the start and end points to their original
positions by using a right mouse click on the event triangle that you have moved
and selecting Reset to Original Position from the displayed menu.
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Editing the Method
If you reintegrate now after restoring the valley point to its original position, you
should get the initial integration results. After examining the reintegration results,
close the Results window.
Editing the Method

Now let’s look at some of the changes you can make to the method and how they
affect the results. This time, leave the Results window open. The Results
window contains the chromatographic results calculated for this data file. In
addition to the injection time and date, the report lists the time and date of the
last recalculation done and the method used to do it.
The Results window can be positioned, scrolled, and sized.
Now, let’s change the method so that the peaks are measured in units of peak
height rather than peak area.
Select Edit Method >Integration Parameters... . The Integration Parameters
dialog box is displayed.
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The Integration Parameters dialog box is partitioned into sections associated with
the various functions of peak detection, measurement, and result calculation.
Notice that the Results window is automatically hidden while you work on the
method.
Click on Peak Height within the Peak Measurement section of the Integration
Parameters dialog box. The Peak Height radio button becomes dark (selected).
Click on Save.
This saves the settings for this window temporarily, but it does not write them to
the method.
To reintegrate the file according to the new method, select Results >Reintegrate
Now. A dialog box is opened that asks if you want to save the changes to the
current method before reintegrating. Click Yes.
Open the results window by right-clicking on the chromatogram trace. Notice that
both the Result (%) and the number of counts (now in peak height units) have
changed for each peak.
Close the Results window and return to the Interactive Graphics/Data Handling
window.
To end your Interactive Graphics session, select File >Exit.
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Recalculating in System Control

You can use a sequence in System Control to reprocess one or more
chromatographic data files. This lets you adjust chromatographic conditions after
you’ve made a sequence of injections.
Because recalculations do not require the use of any instrument modules, you
can recalculate with any instrument, even one with no modules assigned to it.
1. Opening System Control.
Select an unused instrument from the Instrument menu in System Control or
double-click in the box for that instrument in the Instrument Configuration
window. The Instrument’s System Control window opens and displays the
Instrument’s Status.
2. Activating and Editing an Existing Method for Recalculation

Select File >Activate Method.
The Activate a System Control Method File dialog opens. Select the method
file ANOTHER.MTH from the ChromExamples directory and click the Open
button.
Click on the Active Method tab on the Toolbar, which is labeled ANOTHER.MTH
in our case, and select View / Edit Method.
From the Method Builder dialog, highlight the Integration Parameters section
of the method.
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The Integration Parameters window opens, showing the current settings. Peak
measurement is by height, and Report Unidentified Peaks is checked.
Select Peak Area in the peak measurement field.
Select File >Save.
Close Method Builder.
2. Creating a Recalc List for Recalc
Select File >New Recalc List.
Select the ChromExamples directory and type practice.rcl into the file name field.
Click the Save tab. The RecalcList dialog opens.
Click the Add tab and then Browse... .This opens the Open Data File dialog
box.
Find and select the data file called STAR012.RUN in the ChromExamples
directory. Click Open. This file is added to the RecalcList spreadsheet. Click on
the arrow in the Sample Type field. A drop-down menu opens.
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Select Analysis. Leave the other fields set to their default values.
4. Recalculating the Results

Click the Begin tab in the Recalclist dialog. Alternatively, you can select the
menu command Recalculate >Begin Recalc List.
If previously set to “Prompt on Automation Start”, the Instrument Parameters
dialog box appears.
Click in the Operator text box, type your name, then click OK. (If the Instrument
1 Parameters dialog box does not appear, you can open it by selecting
Instrument/Configuration, and click on the Instrument 1 Parameters tab located
in the lower right side of the Configuration window).
A message from System Control appears stating that it will be recalculating

samples in RECALC.SMP using the method ANOTHER.MTH.
Click the OK button to carry out the operation.
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A message appears at the bottom of the window to inform you that System
Control is doing the recalculation. The sample name, the injection number, and
the name of the data file are listed. Wait for the message “End of automation
reached.” This message appears when the recalculation has been completed.
Click the Report button in the active RecalcList window.
The results report is displayed. Look at the Results column. Notice that the
result for each peak is expressed as a percentage of the total area for all the
peaks.
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Tutorial 2 Changing Peak
Detection Parameters
Overview
The Workstation provides several ways to change how peaks are detected after
a run. You can modify settings in the Peak Detection area of the Integration
Parameters window, or you can use the Time Events Table to program changes
in Peak Width or inhibit integration. All such changes require reintegration with
the new method. Both System Control and Interactive Graphics/Data Handling
allow these changes. For this tutorial, you will use Interactive Graphics.
Topics Discussed
• Changing the Initial Peak Width
• Changing the Signal-to-Noise Ratio
• Changing the II and WI Time Events
Preparing the Data File for Use with this Tutorial

Because PRACTICE.RUN is used for several tutorials, you should copy this data
file to DETECT.RUN for use with this tutorial.
In Windows Explorer.
1. View the C:\VarianWS\GCEXAMPLES directory.
2. Use the right mouse button to click on PRACTICE.RUN, and select Copy.
3. Select EDIT >Paste. A copy of this file is added at the end of the list.
4. Use the right mouse button to click on the new file. Select Rename, and type
DETECT.RUN.
Opening the Data File and Method

Click on the Interactive Graphics/Data Handling button in the Varian
Workstation toolbar. The Open Multiple Data Files dialog opens.
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Select the detect.RUN data file from the ChromExamples directory and click the
Open File(s) tab.
1. Select menu command File >Open Method in the Interactive Graphics
window, then double-click on method file practice.mth.
Notice the title bar of the Interactive Graphics/Data Handling window. The
method is identified as practice.mth.
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Changing the Initial Peak Width

You can now edit the data handling parameters for the method. Before you
make any changes, though, integrate the peaks and examine the results for the
run as they appear initially.
To integrate, use the menu command Results >Integrate Now.
1. To open the results file click on the chromatogram trace with the right mouse
button and select View Results Only as seen in the menu below.
The results for the data file appear. Note the areas for the peaks at 3.392 and
3.471 minutes. The results should appear as shown below.
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Now, let's take a look at the Initial Peak Width setting and its effect on how the
peaks are processed.
2. Close the Results window.
3. Select the menu command View >Locator Window (make sure it is
checked).
4. Select View >Main Toolbar (make sure it is checked).
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5. Zoom in on the area from 0.5 to 4.0. To zoom, highlight the desired area in
the locator window or highlight the region in the main window from 0.5 to 4.0.
(Areas of the display can be highlighted by clicking on the upper left hand
corner of the region you wish to zoom with the left mouse button, dragging
the mouse to the lower right hand corner of the area you wish to display, and
releasing the mouse button.)
Notice the placement of baselines and peak event markers.
Select Edit Method >Integration Parameters... .

The Integration Parameters dialog box appears.
1. Increase the Initial Peak Width value from 4 to 32 by clicking on the up arrow
until 32 appears in the box.
2. Choose Save to close the Integration Parameters dialog box and return to
the Interactive Graphics/Data handling window.
3. Select Results >Reintegration List...
Note that a check mark appears in the Run DH check box for the data file.
1. Click on the Calculate Results tab. A dialog box appears that asks if you
want to save changes to the current method before reintegrating. Click Yes.
After peak processing has been completed, examine the new set of peak events
displayed in the Zoom window. Notice that for the narrow, early eluting peaks
the event markers have shifted to the right and that three of the peaks do not
have apex peak event triangles on them. This suggests that the Initial Peak
Width value is too large relative to the narrow widths of these peaks. Obviously,
it is important to set the Initial Peak Width small enough so that narrow, early
eluting peaks are properly detected and their peak events are accurately marked.
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Again, view the results by right-clicking on the chromatogram trace and selecting
View Results Only.
Maximize the Results window and examine this new set of results.
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Changing the Signal-to-Noise Ratio
Compare this to the original results. You will notice that the retention times are
slightly shifted and only 8 peaks are reported. The fused peaks at about 3.4
minutes are now reported as one peak. Also, only one peak was detected
between 1.0 and 1.5 minutes. The total number of detected peaks is now 10.
When experimenting with peak processing in the Interactive Graphic/Data
Handling application, it is convenient to leave the Results window active. Then,
after any Reintegration, this window is automatically displayed.
Changing the Signal-to-Noise Ratio

1. Select the menu command Edit Method >Integration Parameters....
2. Decrease the S/N Ratio from 5 to 1.
3. Set the Initial Peak Width back to 4.
4. Choose Save to close the Integration Parameters window.
You can reintegrate the data file quickly if you know that you want to use the
settings in the Reintegration List that you used last time.
1. Choose Results >Reintegrate Now.
2. Click on Save to save the changed method.
Many peak event markers for small peaks have appeared. The lower S/N Ratio
caused peak processing to detect the smaller signals as peaks.
Check the final Results of this change in the S/N Ratio.

Maximize the Results window and take a look at the new set of Results.
They should match the ones below. Note the high number of detected peaks.
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Now, the detected peaks correspond to all signals larger than the new S/N Ratio.
The change in S/N Ratio affects the placement of peak events and baselines, the
accuracy of which are necessary for reliable chromatographic quantitation.
Setting the correct S/N Ratio is particularly important in percent calculations,
where the results for each peak are expressed as a percentage of the total area
or height counts for all the peaks.
NOTE: To restore the data handling on this file for the next tutorial, increase the
S/N Ratio from 1 to 5 and reintegrate the data file.
Changing the II Time Events

A method can include a set of time-programmable events to tailor the integration
and peak area allocation functions for a particular run. In this section, we will
examine how Inhibit Integrate (II) affects peak detection. Other Time-
Programmable events are discussed in a later tutorial.
Double-click in the Chromatogram window to restore the Zoom window to the full
range of the run file.
In addition to the positions of the peak events, Interactive Graphics also indicate
the positions of time events to help you interpret how your chromatogram is
being processed. Since no time events have been programmed yet, none of
these markers should appear.
Select View >Preferences.
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Changing the II Time Events
Make sure the Show Method Editing Panel box is checked. Click on OK to
confirm the choice and close the dialog box.
Select Edit Method >Time Events. The Time Events Table window is
displayed.
NOTE: For an exercise in how to graphically enter Timed Events, see Tutorial 5
Now, let's add a time event to inhibit integration at the beginning of the
chromatogram.
1. Click on Add, to add a new line of default entries.
2. Click the arrow at the right of the Event box.
3. Click the up or down scroll arrow until II appears. Click the II event.
4. Change the start time and end times. Enter 0.01 into the Time column and
1.80 into the Value/End Time column.
Your display should look like the following.
Choose Save to close the Time Events Table window. This will display the Time
Event Window below the chromatogram trace.
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Select Results >Reintegrate Now. Save the changed method before
reintegration.
After the calculation, the plot will be updated to reflect the changes in the time
program. The figure above shows the updated chromatogram. Notice that no
peak event markers appear at the beginning of the chromatogram. Also, the
Time Events annotation on the display has been updated with green boxes near
the baseline at the start and end times for the II event.
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Changing the WI Time Event
Changing the WI Time Event

Now, suppose you decided not to use the II event but wanted to program some
changes in the peak width.
1. Open the Time Events Table window again by selecting Edit Method >Time
Events. The II line in the spreadsheet is selected (active).
2. Click the down arrow at the right of the Event box.
3. Press the down arrow and select WI to replace the II event.
4. Change the start Time to 5.0 and the Value/End Time to 64.
5. Click on Add. Set the new WI event start Time to 4.0 and the Value/End
Time to 32.
When you add a line for an earlier time event, use Sort to move it to the correct
position in the table.
Click on Sort. Your display should look like the following display.
Select and Delete the WI event at 5.00 min.

Choose Save to close the Time Events Table window.
Select Results >Reintegrate Now and save the changed method before
reintegration.
You must Reintegrate as before because you made changes that affect peak
integration. After the calculation, the plot will be updated to reflect the changes in
the time program. Notice that the Time Events annotation on the display has
been updated with a light blue box near the baseline at the start time for the first
WI event.
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Place the cursor on the WI Time Event marker.
The Time Event information box is displayed below the marker showing the event
type, its program time, and the actual time of execution.
Open the Results window by right-clicking on the chromatogram trace and
selecting View Results Only. The small peaks at the beginning of the file are
once again detected and included in the report. Their peak event markers should
be correctly placed. The peaks that eluted after four minutes were not integrated
correctly because the Peak Width setting was too high. Peak processing does
not correct for this because the automatic Peak Width updating was turned off
once you made a WI time program. Whenever you time program Peak Widths,
you must make all the appropriate changes over the length of the run.
The other Time Events can be programmed just as the II and WI events were.
Close the Results window to return to the Interactive Graphics/Data Handling
window.
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Tutorial 3 Filling a Peak Table
Overview
Peak tables contain the peak-specific information necessary for the execution of
most data handling, peak processing, and quantitative operations. Using
Interactive Graphics, you can easily create a peak table for any chromatographic
data gathered with the Workstation. This tutorial covers the basic steps for filling
the Peak Table.
Topics Discussed
• Opening the Peak Table window
• Adding peaks
• Naming peaks
• Designating peak functions
• Entering amounts for calibration levels
• Editing the Peak Table
• Setting calibration options

Because Practice.RUN is used for several tutorials, you should copy this data file
to Table.RUN for use with this tutorial.
1. Open Windows Explorer.
2. View the C:\VarianWS\ChromExamples directory.
3. Use the right mouse button to click on Practice.RUN, and select Copy.
4. Select Edit >Paste. A copy of the file is added at the end of the list.
5. Use the right mouse button to click on the new file. Select Rename, and type
Table.RUN.
Opening the Fill Peak Table Window

Open Interactive Graphics by clicking on the Interactive Graphics bar in the
Workstation Toolbar.
Double-click on Table.RUN from the ChromExamples directory and choose OK.
Select File >Open Method.
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Choose the ChromExamples directory and double-click on Practice.MTH.
After you make Table.RUN the active chromatogram and Practice.MTH the
active method, you can open the Fill Peak Table window.
Select Edit Method >Fill Peak Table.
The Fill Peak Table window appears.
The Fill Peak Table window can be moved anywhere on the window. Just click
on the title bar and drag it to the desired position. For now, move the Fill Peak
Table window to the upper part of the screen.
Adding Peaks with the cursor

Now, you can begin to add peaks to the Peak Table. Notice the small, triangular
event markers on the chromatogram indicating each peak start, peak apex, and
peak end. You can add a peak to the Peak Table by clicking anywhere between
its peak start and peak end event markers.
Move the cursor to the Zoom window, and click anywhere between the start and
end markers of the first peak eluting at about 1.0 minutes.
The first line of the Peak Table now displays the retention time for this peak. The
Peak Name field contains the default name.
Click between the peak start and peak end markers for the peak eluting at about
2.8 minutes. Check to see that the peak is entered.
Now, click on the peak eluting at about 2.0 minutes.
Continue filling the Peak Table until all the peaks are listed.
Do not enter the peaks at 1.05, 1.11 and 3.47 and 7.4 minutes.
Click on Sort. When you look at the Peak Table, you will see that the peaks
have been reordered according to their retention times.
Select Save.
Adding Peaks from a selection

You can also add all peaks contained within a selection. A selection is the area
selected during zooming.
Click on the box marked Fill table from selection which is located on the Fill
Peak Table dialog.
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Naming Peaks
Move the cursor to the Zoom window, click on the left upper corner of the area
you wish to select (start at .5 minutes) and click and hold left mouse button.
Drag the mouse to the lower right hand corner of the area you wish to select (end
at 6 minutes) and release the mouse button.
Peaks are automatically entered into the peak table. Care should be used when
using this command because any integrated peak within the selected range will
be added to the peak table.
Naming Peaks
Select Edit Method >Peak Table. This displays the Peak Table Window.
As you added peaks to the table, the software supplied unique default names
based on the peak retention times. When you have added all the peaks to the
Peak Table, you can edit each Peak Name and supply more descriptive names if
you wish.
Click on the Peak Name field for the first peak.
Type First Peak.
As you type, the Peak Name field is cleared and the name First Peak replaces it.
Press the Down Arrow key on your keyboard. The Peak Name field for the
second peak is now highlighted. Type Second Peak. Press the Down Arrow Key
again.
This is a faster way of entering data than to select fields by a click of the mouse.
Rename the third peak Internal Standard. Press the Down Arrow key.
Continue renaming the remaining peaks.
Your table should look like the one shown.
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Designating Peak Functions
You can designate certain peaks to perform specific functions. The check boxes
in the Peak Table are used to select the following functions:
Heading Peak Type Function
Ref Reference Peak Used to adjust the peak identification retention
time windows for changes in chromatographic
conditions that may cause retention times to
drift.
Std Internal Standard Peak Used as an internal standard peak for the
calculation of results with an internal standard
or by normalized %.
RRT Relative Retention Time Used as a reference from which the relative
Peak retention times of other peaks are calculated.
Reference Peak(s)
Click in the Ref check box for the peak named Sixth Peak.
A check mark appears in the Ref box to indicate that it has been selected.
Click the Ref box for the peak named Internal Standard.
The Ref box for this peak is also selected. You may choose to have more than
one reference peak.
NOTE: If more than one peak appears in the reference peak time window, the
largest peak in the window is selected as the Reference Peak.
Internal Standard Peak(s)

An internal standard peak is used in the calibration process needed for
quantitative determinations. You can designate up to eight peaks as Internal
Standard Peaks.
NOTE: Refer to Run File Tutorial 7 for further information on calibrating with
multiple internal standards.
Click on the Std box for the third peak, named Internal Standard. It is now
indicated in the Standard Peak Name column that the third peak is designated as
the Internal Standard peak for the calculation of results for all other peaks in the
table.
Relative Retention Time Peak

The RRT peak is used, in association with the unretained peak time, to calculate
relative retention times for all identified and reported peaks. Only one peak can
be designated the Relative Retention Time Peak.
Click the RRT box for the peak named First Peak.
The RRT box is now marked for the first peak.
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Editing the Peak Table
Entering Amounts for Calibration Levels

Use the horizontal scroll bar to view the Amount columns. You can examine and
enter amounts for up to ten different calibration levels. Each level corresponds to
a calibration mixture. The value entered for each peak is the known, measured
amount of that compound in the standard. The calibration levels are used in
verification and calibration runs.
1. Click the horizontal scroll bar to move through the ten levels.
2. Click on the Level 1 Amount cell for the first peak. The default value is
highlighted.
3. Click on the Level 2 Amount cell for the first peak in the peak table.
4. Enter 2.0.
To set all peaks to the same values as the first peak, you can enter the value for
each peak, or take advantage of the Fill Down function: Click on the box labeled
'Level 2 Amount'. The whole column is now highlighted. Click on the 'Fill Down'
button and observe that the value for the first peak is copied to all peaks.
Repeat the previous operations to set Level 3 to 4.0, Level 4 to 8.0, Level 5 to
16.0, and Level 6 to 32.0 for each peak in the peak table.
The peak table should look like the one shown.
Editing the Peak Table

On the right side of the Peak Table there are three edit buttons: Delete, Add,
and Insert. These buttons allow you to edit the Peak table.
Click anywhere on the line for the peak named First Peak.
Now click the Insert button.
A new line is displayed just before the selected line. Each level for the inserted
peak has been assigned a default value of 1.
Click anywhere on the line for the Internal Standard peak.
Click the Insert button.
A new line is now displayed just before the Internal Standard entry, with a
Retention Time of 1.977 and default values of 1 for all Amounts levels.
Click the Delete button. The selected Peak Table entry is removed.
Select the entry inserted at the top of the Peak Table by clicking anywhere in that
line.
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Click the Delete button again. The entry inserted at the top of the Peak Table is
deleted.
Now, save the contents of the Peak Table you just created.
Click the Save button to close the Peak Table Window.
Select File >Save Method As.
Type the method name, Table.mth, in the file name field and click Save.
If you were to use this method to execute any data handling or quantitative
operation, the Peak Table you have just created would be used.
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Tutorial 4 Identifying Peaks
Overview
A chromatographic data file contains all of the raw data points collected for one
injection. The Workstation's data handling system identifies any peaks detected
in the raw data based on their retention times. The workstation allows you to
create and adjust time windows, which define ranges of retention times in which
peaks are to be identified. Time windows can also be used to eliminate from
reports those peaks that have no analytical significance.
Topics Discussed
• Peak Windows
• Time Windows
• Showing Peak Windows
• Changing Peak Functions
• Peak Reject
• Reporting Unidentified Peaks

Because Table.RUN is used for several tutorials, you should copy this data file to
Ident.RUN for use with this tutorial.
In Windows Explorer:
View the C:\VarianWS\ChromExamples directory.
Use the right mouse button to click on Table.RUN, and select Copy.
Select EDIT >Paste. A copy of this file is added at the end of the list.
Use the right mouse button to click on the new file. Select Rename, and type
Ident.RUN.
Peak Windows
Since chromatographic retention times are not absolutely precise, you specify a
window of time (a peak window) for the Workstation to identify a particular peak.
The peak window is the actual span of time on the chromatogram that the
software searches. The software will only identify a peak if it falls within the peak
window.
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Open the Interactive Graphics/Data Handling application by clicking on its button
in the Workstation Toolbar.
Select the data file Ident.RUN in the ChromExamples directory, and press the
Open File(s) button.
Select File >Open Method...
Select IDENT.MTH from the ChromExamples directory.
Choose Edit Method >Peak Table...
The Peak Table associated with this data file appears. Notice that eight peaks
are listed in the Peak Table.
Choose Save or Cancel, and return to the Interactive Graphics/Data Handling
window.
Select Results >Reintegrate Now. Save the Method before reintegration.
To view the results, click on the chromatogram trace with the right mouse button.
Select View Results Only.
Your window should look like the one below.
All peaks in the Peak Table are identified. There are 719661 unidentified counts
for peaks not listed in the Peak Table.
Define Peak Windows

Each peak window is determined by a time window that you enter. The time
windows are both added to and subtracted from the expected retention times to
define the peak windows.
The workstation recognizes two types of time windows; one for reference peaks
and one for all other peaks. Peaks in the two window types are identified
differently. For reference peaks, the largest peak in the window is considered the
reference peak. For other peaks, the one closest to the center of the peak
window is identified as the peak.
You set the time window sizes in the Define Peak Windows dialog box, which is
accessed from the Peak Table dialog. Close the Results window. Select the
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Showing Peak Windows
menu command Edit Method >Peak Table and click on the Define Peak
Windows tab.
The time window used to identify a peak is an absolute width in minutes plus a
relative width expressed as a percentage of the peak's retention time. You may
set either the absolute or relative time window to zero.
The default values for both “reference peaks” and “other peaks” are: time window
width of 0.1 minutes plus a Retention Time of 2%.
Keep the default values and click the Save tab to exit the Define Peak Windows
dialog and click Save again to exit the Peak Table window.
Showing Peak Windows

In Interactive Graphics, you have the option of displaying the peak window for
each of the peaks in the Peak Table.
Select View >Visual Method Edit Window, to show the peak window for each of
the peaks in the peak table.
The chromatogram should look like the one shown. Identifying color bars appear
under each peak that has been entered in the Peak Table. The default colors for
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the different peak window bars are:
Standard peaks: Red Relative Retention Time peak: Green

Reference peaks: Blue Other peaks: Yellow
Changing Peak Functions

You can change the peak functions easily in the Peak Table.
Select Edit Method >Peak Table.
Click in the Ref. box for the fourth peak to make it the reference peak.
Click Save to return to the Interactive Graphics window.
Look at the color bars under the peaks. The fourth peak now has a blue
Reference Peak indicator bar. The third peak, a standard peak that is also a
reference peak, is marked with stripes of blue and red.
Select Edit Method >Peak Table, deselect the Ref box for the internal standard
peak.
Click Save to return to the Graphic window. The third peak is now marked by a
red bar.
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Unidentified Peaks
Peak Reject
Often, over the course of a chromatographic run, numerous peaks appear that
are not of interest to you. While these peaks might be detected, there is no need
to report them. There are several ways to tailor a peak processing method so
that only the peaks of interest are reported. One of these is by adjusting the Peak
Reject parameter: peaks smaller than the Peak Reject value are eliminated from
the final report.
Select Edit Method >Integration Parameters.
Set the Initial Peak Reject value field to 50000.
Now, peaks smaller than 50000 counts will not be included in the Results file.
Press Save to exit the Integration Parameters dialog.
You'll need to recalculate the Results file so that this new Peak Reject value is
used in the results.
Select Results >Reintegrate Now. (You can also select the “Reintegrate Now”
button from the Toolbar) and save the changes to the current method
before reintegrating, in the Interactive Graphics dialog that opens.
Take a look at the Results now.
Open the Results Report by clicking with the right mouse button on the
chromatogram trace.
When the Results window appears, enlarge it so that you can see the results of
this recalculation.
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Unidentified Peaks
Often, a chromatogram will contain peaks that are not of analytical interest but
are as large as, or larger than those peaks that are of interest. In these cases,
adjusting the Peak Reject value is inappropriate; you would lose both important
and unimportant peaks from the report. The Interactive Graphics/Data Handling
application provides another means to focus a report on the peaks of interest.
You can turn off reporting of unidentified peaks.
Select Edit Method >Integration Parameters again.
Click once in the box labeled Report Unidentified Peaks so that this option is no
longer selected. Press Save.
Only identified peaks will now appear in the Results file.
Select Results >Reintegrate Now to recalculate the data file using this new set
of parameters.
Open the Results window by right-clicking on the chromatogram trace.
The list of reported peaks is considerably shorter now. It includes only those
peaks corresponding to “identified peaks” in the Peak Table and does not include
other peaks, even those that are larger than the Peak Reject value. Here, only
peaks identified within their respective retention time search windows are
included in the final results file.
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Tutorial 5 Using the II, SR, and VB
Time Events
Overview
You can use the Time Events Table to program several peak processing
changes over the time of a chromatogram. The Inhibit Integrate (II), Solvent
Reject (SR), and Valley Baseline (VB) time events can help you optimize peak
detection and calculation of results. Both System Control and Interactive
Graphics/Data Handling allow these changes. For this tutorial, you will use
Interactive Graphics.
Topics Discussed
• Inhibiting Integration
• Using Solvent Reject
• Using Valley Baseline
• The effects of Other Peak Processing Events on VB
Inhibiting Integration
An Inhibit Integrate (II) event is a time programmable event that can be used to
turn off integration in selected regions of the chromatogram. The Inhibit Integrate
event is used to:
Eliminate from a report those peaks that are not of interest.
Avoid improper baseline assignment during periods when the baseline might be
distorted, such as during the switching of sampling valves.
Force or create a baseline where needed in the chromatogram.
The Inhibit Integrate event suppresses integration of peak area or height
between the start and end time of the event. The II event forces the baseline to
be drawn to the point where the II event starts and the baseline to start drawing
at the point where the II event stops. When II is active, peak processing is
disabled. This does not mean that raw data is not being stored; it simply means
that it is not being integrated. If you remove the II event, integration is turned
back on when you recalculate the stored data file.
If it is not already opened, select the Interactive Graphics/Data Handling
application from the Varian Workstation toolbar.
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Find and open the data file STAR012.RUN in the ChromExamples directory from
the Open Multiple Data Files dialog.
The data file now appears, and the chromatogram should look like the one
shown.
Select the menu command File >Build Method from Datafile.
A Save As dialog box will ask you to provide a name for the method you are
using. Type in star012.mth and click on OK.
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Editing a Time Event from the Menu
This command opens the Workstation method that was last used to process the
data file.
You will edit the Time Events Table to see how Inhibit Integrate works. This
example illustrates how the II event critically affects the placement of the
chromatographic baseline. The baseline used in this example is not intended to
represent proper baseline placement.
Select Edit Method >Time Events. The Time Events dialog box appears.
Editing a Time Event from the Menu

Now, let's program the Inhibit Integrate (II) event to start at 3.5 minutes and stop
at 4.1 minutes.
Click on Add.
Click on the down arrow at the right of the Event box.
Scroll through the Event types and select the II. Set the Start time to 3.5 and the
End time to 4.1.
The Time Events Table should match the following figure.
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Choose Save to close the Time Events Table window and return to the
Interactive Graphics/Data Handling window.
Changes to the II event must be followed by a Reintegration.
Select Results >Reintegration List.
The Run DH check box for STAR012.RUN is checked.
Click on the Calculate Results tab and save the changes to the method in the
dialog that opens.
The Workstation begins processing the file. After Reintegration is complete, look
at how the new II event has affected the chromatographic data file. A baseline
has been forced at the points where II is turned on and off. Also, notice that the
peak at about 3.7 minutes is not detected and does not have peak event marks.
Changes in the II event also alter the final Results for a chromatographic data
file.
Open the Results window by right-clicking on the chromatogram trace and
selecting View Results Only.
Enlarge the Results window and examine the Results.
They should appear as in the following figure.
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Graphical Placement of a Time Event
Compare this to the original results shown in the following figure. Observe that
the peak originally detected at about 3.7 minutes is now eliminated from the
report. Also, notice how the area counts have changed as a result of the new
baseline placement.
If you were to delete the II event from the Time Events Table and then perform a
Reintegration, the peak at 3.7 minutes would again be detected.
Graphical Placement of a Time Event

You can graphically edit the II Event in the interactive time events window. When
the time events window is shown below the chromatogram, try using the left and
right mouse buttons to edit the events.
Close the Results window.
Select the menu command View and check Visual Method Edit Window. The
interactive time events window now appears below the chromatogram.
Place the cursor on the II event in the interactive window. A small window is
displayed providing you with information on the event.
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You can move the II event by clicking and dragging the triangles marking the
start and end times.
Use the right mouse button to click on either the triangle or the connecting line
marking the II event.
Select Delete (II) from the menu. The II event is deleted from the Interactive
Time Event window and also from the Time Events Table. Now you can
reintegrate the data file without the II event.
Select the menu command Results >Reintegrate Now. Save the changed
Method before reintegration.
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Using Solvent Reject
Notice that the peak at 3.7 minutes is now detected in the chromatogram and
included in the Results report.
Using Solvent Reject

In this section, you will see how the Inhibit Integrate (II) function differs in
performance from the Solvent Reject (SR) function.
Select the menu command Edit Method >Time Events..
When the Time Events Table appears, note that the II event is no longer listed.
Click on Add to enter a new event into the table.
Click on the down arrow in the Event box. Scroll through the Event types and
select Solvent Reject (SR). Set the start and end times again to 3.5 and 4.1
minutes.
The table should look like the one in the following Figure.
Press Save to close the Time Events Table window.

It's time to implement the new change to the peak processing method. Since the
settings in the Reintegration list would be the same as they were the last time
you used it, you can use the Reintegrate Now shortcut.
Select the menu command Results >Reintegrate Now and save the changes to
the method before reintegration.
After peak processing has been completed, the plot will be updated to reflect the
changes in the time program.
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Notice that the SR function does not affect baseline placement or peak detection.
Thus, the plot looks similar to the original data file used at the beginning of this
tutorial. Solvent Reject eliminates peaks from reports but does not influence their
detection, or affect baseline placement.
To open the results file click on the chromatogram trace with the right mouse
button and select View Results Only.
Enlarge the Results window and take a look at the previously missing peak.
The results should look like those in the following figure.
Solvent Reject operates as a post-integration filter. It rejects detected peaks

whose apices fall within the SR window. It will not affect tangent separations,
baseline placement, or Peak Width updating. In contrast, II affects all three of
these functions by changing where baselines are established.
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Using Valley Baseline
Using Valley Baseline

A Valley Baseline (VB) event creates a time window within which all valley points
are forced to behave as baseline points for peak integration. Now, take a look at
how the VB event functions.
Select File >Open Method.
Select the method file VB.MTH from the ChromExamples directory.
To ensure that the integration for STAR012.RUN is at the proper starting point,
reintegrate this data file with the new method.
Select Results >Reintegrate Now.
The chromatogram should look like the one shown.
Use the Interactive Time Events to add a Valley Baseline (VB) event, and to set
its start and end times.
With the right mouse button click on the Visual Method Edit Window.
Click on VB: Add Valley Baseline.
The VB event is now displayed in the Visual Method Edit Window below the
chromatogram. The event is also entered in the Time Events Table. Now edit
the start and end times.
Use the right mouse button to click on either the triangles or the connecting line
marking the VB event.
Click on Edit (VB).
The displayed Time Events Table now lists the VB event.
Set the start Time to 0.01 minutes and the Value/End Time to 9.00 minutes.
Your table should look like the figure shown.
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Choose Save.
Select the menu command Results >Reintegrate Now and save the changed
method before reintegrating.
The chromatogram should look like the figure below.
Notice that the baseline has been drawn to all valley point events. This is not a
good baseline assignment, however, so change the VB event to achieve a better
integration of this chromatogram.
Open the Time Events Table window again.
Change the VB time event Start from 0.01 minutes to 0.5 minutes. Change the
End time from 9.00 minutes to 3 minutes.
Select Save to exit the Time Events Table window.
Select Results >Reintegrate Now as before.
Observe the change. Only the first three peaks have been forced to baseline
resolution.
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The Effects of Other Peak Processing Events on VB
Other peak processing events can affect the Valley Baseline parameter and the
baseline assignment. Now, take a look at the effect of changes in the tangent
height threshold (T%) on the baseline assignment.

Zoom the chromatogram to expand the area between about 5.5 and 8.5 minutes
as shown below.
Select the menu command View >Preferences. Click the tab for Trace Settings
and check the Show Cursor >Peak information field. Click on OK.
Select the menu command View and check Visual Method Edit Window.
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The current Tangent Height Percent threshold is 10%. Notice that, at this setting,
the peak at 7 minutes is skimmed as a tangent peak.
Move the cursor to the peak event marker at about 7.7 minutes. Notice that this
event is identified as the end of a tangent peak (Tangent Pk. End).
With the right mouse button click on the Visual Method Edit Window.
Click on VB: Add Valley Baseline.
A new VB event is now displayed in the Interactive window and also added to the
Time Event Table.
Use the right mouse button to Click on one of the triangles or the connecting line
marking the new VB event.
Click on Edit (VB).
In the displayed Time Events Table, set the start Time for the new VB event to
4.5 minutes and the End Time to 9.0 minutes. Choose Save.
Select Results >Reintegrate Now. Save the Method.
Notice that the baseline for the peak at about 7 minutes is now drawn from the
valley point to the peak end event, and the Tangent Pk. End event is essentially
ignored.
So, when you use a VB timed event in an area with skimmed tangent peaks, be
aware that the tangent peak events are treated as non-events and that an
improper baseline assignment may be drawn.
Changing the Signal-to-Noise Ratio (S/N Ratio) can affect integration by
changing the current peak sensing events or introducing new peak sensing
events. This can occur whether a VB event is present or not.
Select View >Chromatogram Toolbar. (Make sure that this menu item is
checked).
Click on the icon below to normalize both the x and y axis of the plot.
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Zoom the chromatogram from about 0.5 to 3.5 minutes.

Select View >Preferences. Select the Trace Settings tab and then check the
box named Show cursor / peak information. Then click on the OK button.
Move the cursor to the peak at 1.75 minutes.
The Chromatogram should look like the figure shown.
Click on the peak event marker at about 1.6 minutes and notice that it is a valley
point.
Select the menu command Edit Method >Integration Parameters.
Decrease the S/N Ratio to 1 and click Save.
Select Results >Reintegrate Now. Notice that many baseline noise events are
now present.
A low S/N Ratio can introduce noise-produced peak events, which can affect the
integration of the peaks of interest. Likewise, a high S/N setting can change a
peak event to a different type of event, which can then affect integration.
Select Edit Method >Time Events. Delete the first VB event.
Increase the S/N Ratio back to 5.
Reintegrate again.
Close Interactive Graphics.
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Tutorial 6 Calibrating with an
External Standard
Overview
Calibrating with an external standard is a two-step process. First, you perform
calibration runs with known amounts of the analytes of interest. This determines
the response curve for the analytes with the detector to be used for the analysis.
Coefficients for the calibration curve are calculated during this run and saved in
the method. After this is done, you can make analysis runs with unknown
amounts of the calibration analyte to determine the composition of your sample.
The response curve for each analyte is based on an absolute amount of injected
material; it is not relative to any other component in the run.
Topics Discussed
• Generation of Calibration Data
• The Calibration Curve
Generation of Calibration Data

Calibration with an External Standard requires that calibration data for each
compound be present in the method peak table. This data is generated in
calibration runs and saved in the method. The method is then used to perform
an analysis of the sample. As many as ten concentration levels can be used to
generate a calibration curve for the analytes of interest. This tutorial uses only
four different levels in five data files.
Open Interactive Graphics from the Workstation Toolbar.
The Open Multiple Data Files window appears.
Choose the chromatographic data file CAL_1.RUN in the ChromExamples
Select the Add To List tab.
You may double-click on a data file to quickly add it to the list.
Continue adding the following data files to the list: CAL_1A.RUN, CAL_2.RUN,
CAL_3.RUN, CAL_4.RUN.
Channel B should be selected for all data files in this series.
The analytical run for this tutorial is called ANALYSIS.RUN. The file called
VERIF_3.RUN is a verification run for this series.
Add ANALYSIS.RUN and VERIF_3.RUN to the list and press Open Files.
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The IG screen should look similar to the figure shown.
If the chromatograms display looks different, make sure the Overlay

Chromatograms button is checked and not the Tile Chromatograms button
. Also, select the menu command View >Preferences and press the Offsets
tab in the Interactive Graphics dialog.
Select the Ampli 5%, Time 3% tab and then close the dialog by clicking OK.
Next, you will load the method file, which will be used for the analysis. You will
use the method file, EXT_STD.MTH, located in the ChromExamples directory.
The information in the peak table is necessary to generate the coefficients of the
calibration curve.
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Select the menu command File >Open Method. Find and select the method file
EXT_STD.MTH in the Open Method dialog, and press the Open tab.
The title bar for the Interactive Graphics window now lists EXT_STD.MTH as the
active method.
Now, verify the calibration parameters to be used, as follows:
Select Edit Method >Calibration Setup.
The Calibration Setup window opens.
The window should look like the one shown next. The Calibration Type should
be External Standard. The Number of Calibration Levels should be set to 4. The
Curve settings should be Linear, Ignore.
Select Save to return to the Interactive Graphics window.

Now, verify the Peak Table settings.
The window should look like the one shown next. Verify the seven peaks have
the amounts shown for Levels 1-4.
Click the Save button to close the Peak Table window.
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Next, you will set the Verification Deviation Tolerance for the VERIF_3.RUN
example.
Select Edit Method >Verification Setup. Set the Deviation Tolerance to 15%
and the Out-of-Tolerance Action to No Action.
Save this setup.

Now, you will use the Reintegration List to reintegrate the data and create the
calibration curves.
Select Results >Reintegration List...
The Reintegration List appears.
The data file for each chromatogram displayed in IG appears here. The fourth
column in the Reintegration List is the Sample Type, which must be set as
Calibration for the first five files, Analysis for the sixth and as Verification for the
last one.
Set the Sample Type for each of the first five data files to Calibration.
Click in the cell for each file and pull down the drop-down list box. Click on
Calibration.
Set the Sample Type for ANALYSIS.RUN to Analysis, and VERIF_3.RUN to
Verification.
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The Calibration Curve
The fifth column is the Calibration Level column. Each value listed here
corresponds to a Level column in the peak table. The calibration levels used in
this tutorial are numbered 1 through 4
Set the Cal. level for CAL_1.RUN and CAL_1A.RUN to 1, CAL_2.RUN to 2,
CAL_3.RUN to 3, and CAL_4.RUN to 4. This associates the amounts entered in
the Peak Table with the runs that contain those amounts.
Set the Cal. Level for the VERIF_3.RUN to 3.
Click the scroll bar to scroll past the list of values for the Internal Standard,
Multiplier, Divisor, and Unidentified Peak Factor. Leave them set to their default
values.
Each chromatogram listed should have its Run DH box checked, which means
that the data in that data file will be recalculated. If you want to exclude a file
from the recalculation, you can clear its Run DH box by clicking in it. The
Reintegration List should look like the example shown.
Make sure that the Clear Coefficients at Start of List option is selected.
Click the Calculate Results button.
Select Yes to the message, “All calibration coefficients will be cleared -
continue?”.
An information box appears with the message, “Processing CAL_1.RUN.” The
message changes as each data file is processed.

When the data has been processed, examine the Calibration Coefficients that
have been generated for each peak. These coefficients describe the equation for
the calibration curve for each compound.
Click on the Edit/Lock Calibration Data… button at the bottom of the window.
The Coefficients window should look like the one shown next.
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Click Cancel to return to the Calibration Setup dialog.
Click on the View Curves... button to see the calibration curve for the first peak.
The Calibration Curve window appears. The peak name appears highlighted in
the Peak Name area and in the title bar.
The Y axis of the calibration curve corresponds to peak size. The X axis
represents the amount of the compound injected.
Click the drop-down menu arrow in the Peak Name field.
Click on the name of the second peak (1-Octanol).
The calibration curve for the selected peak appears in the Calibration Curve
window. The peak's name appears in the title bar.
Continue through the list of peaks until you have seen all the calibration curves.
Use the drop-down menu or the keyboard Up/Down arrows to select each peak.
NOTE: Refer to the tutorial, “Calibrating with an Internal Standard and Getting
Around in the Curve Manager”, for an exercise in using the other curve functions.
Click the Cancel button to return to the Calibration Setup. Click Cancel again to
return to the Interactive Graphics window.
Now you can display the Results Report for any run.
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Click on the white chromatogram trace with the right mouse button. Select View
Results Only.
The Verification Report for VERIF_3.RUN appears. Note that Peaks 3 and 7 are
marked as “Out of Verification Tolerance”.
Close the Results window

Right click anywhere on the plot trace of the sixth chromatogram,
ANALYSIS.RUN (this should be the light blue trace) and select View Results
Only.
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Tutorial 7 Calibrating with Internal
Standards
Overview
Calibrating with an Internal Standard allows you to account for variations in
sample volumes or for loss during sample preparation. You do this by adding a
small, known amount of an additional compound to sets of standards and
samples. Then, you perform calibration runs with the standards. When you
make an injection, any variation in the sample volume is reflected by a detectable
variation in the ratio of areas and amounts for the internal standard. As with
external standard runs, the Workstation plots the calibration curve and uses the
equation for it to calculate results for the analysis runs. The curve is adjusted to
account for the variations in sample volume.
Topics Discussed
• Generation of Calibration Data
• Using the Calibration Curve window
• Using the Calibration Curve options (Curve Manager)

Calibration with an Internal Standard requires that calibration data for each
compound be present in the method peak table. This data is generated in
calibration runs and saved in the method. The method is then used to perform
an analysis of the sample. As many as ten concentration levels can be used to
generate a calibration curve for the analytes of interest. As many as eight
internal standards may be designated. This tutorial uses only four different levels
in five data files and uses two internal standards.
Open Interactive Graphics from the Workstation Star Toolbar.
The Open Multiple Data Files window appears.
Choose the chromatographic data file CAL_1.RUN in the ChromExamples
directory.
Click the Add To List tab.
You may double-click on a data file to quickly add it to the list.
Continue adding the following data files to the list: CAL_1A.RUN, CAL_2.RUN,
CAL_3.RUN, CAL_4.RUN.
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Channel B should be selected for all data files in this series.
The analytical run for this tutorial is called ANALYSIS.RUN. The file called
VERIF_3.RUN is a verification run for this series.
Add ANALYSIS.RUN and VERIF_3.RUN to the list and press Open Files.
The IG screen should look similar to the figure shown next.
Next, you will load the method file which will be used for the analysis. You will
use the method file, INT_STD.MTH, located in the ChromExamples directory.
The information in the peak table is necessary to generate the coefficients of the
calibration curve.
Select File >Open Method and select INT_STD.MTH, press Open Files.
The title bar for the Interactive Graphics window now lists INT_STD.MTH as the
active method.
Now, verify the calibration parameters to be used, as follows:
The Calibration Setup window opens. The window should look like the one
shown next.
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The Calibration Type should be Internal Standard. The Number of Calibration

Levels should be set to 4. The Curve settings should be Linear, Ignore.
Select Save to return to the Interactive Graphics window.
Now, verify the Peak Table settings.
The window should look like the one shown next. Verify the nine peaks have the
amounts shown for Levels 1-4.
Peaks 1 and 8 should be designated as Std peaks. Peaks 2-6 should be

assigned Standard Peak Name, n-Nonane, and peaks 7 and 9 should be
assigned Standard Peak Name, n-Hexbenzene. Any analyte peak can be
assigned to any internal standard.
Click the Save button to close the Peak Table window.
Next, you will set the Verification Deviation Tolerance for the VERIF_3.RUN
example.
Select Edit Method >Verification Setup. Set the Deviation Tolerance to 15%
and the Out-of-Tolerance Action to No Action. Save this setup.
Now, you will use the Reintegration List to reintegrate the data and create the
calibration curves.
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The Reintegration List appears.
The data file for each chromatogram displayed in IG appears here. The fourth
column in the Reintegration List is the Sample Type, which must be set as
Calibration for the first five files, Analysis for the sixth and Verification for the last
one.
Set the Sample Type for each of the first five data files to Calibration.
Click in the cell for each file and pull down the drop-down list box. Click on
Calibration.
Set the Sample Type for ANALYSIS.RUN to Analysis, and VERIF_3.RUN to
Verification.
The fifth column is the Calibration Level column. Each value listed here
corresponds to a Level column in the peak table. The calibration levels used in
this tutorial are numbered 1 through 4.
Set the Cal. level for CAL_1.RUN and CAL_1A.RUN to 1, CAL_2.RUN to 2,
CAL_3.RUN to 3, and CAL_4.RUN to 4. This associates the amounts entered in
the Peak Table with the runs that contain those amounts.
Set the Cal. Level for the VERIF_3.RUN to 3.
Next, you should verify the amounts for the internal standards referenced in the
peak table.
Click on the Amount(s) button for the first data file.
The Internal Standard Amounts window appears.
If the fields are grayed out, click on the Update List button to view the list from
the peak table.
Verify the Amount Standard for the two internal standards as shown next.
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Click on the Save Changes button.

You will need to do this for each of the data files. The amount of internal
standard can vary from sample to sample.
When the data files are reintegrated, these amounts will be placed in the peak
table for use in determining the calibration curves.
Click the scroll bar to scroll past the list of values for the Multiplier, Divisor, and
Unidentified Peak Factor. Leave them set to their default values.
Each chromatogram listed should have its Run DH box checked, which means
that the data in that data file will be recalculated. If you want to exclude a file
from the recalculation, you can clear its Run DH box by clicking on it. The
Reintegration List should look like the example shown.
Make sure that the Clear Coefficients at Start of List option is selected
Click the Calculate Results button.
Select Yes to the message, “All calibration coefficients will be cleared -
continue?”.
An information box appears with the message, “Processing CAL_1.RUN.” The
message changes as each data file is processed.
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When the data has been processed, examine the Calibration Coefficients that
have been generated for each peak. These coefficients describe the equation for
the calibration curve for each compound.
Click on the Edit/Lock Coefficients button at the bottom of the window.
The Coefficients window should look like the one shown next.
Click Cancel to return to the Calibration Setup.

Click on the View Curves... button to see the calibration curve for the first peak
(the internal standard, n-Nonane).
The Calibration Curve window appears. The peak name appears highlighted in
the Peak Name area and in the title bar.
Click the drop-down menu arrow in the Peak Name box.
Click on the name of the second peak (2-Octanone).
The calibration curve for the selected peak appears in the Calibration Curve
window. The peak's name appears in the title bar.
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The Y axis of the calibration curve represents the ratio of the peak size of the
analyte compound to the peak size of the internal standard. The X axis
represents the ratio of the amount of the analyte compound injected to the
amount of internal standard injected.
Continue through the list of peaks until you have seen all the calibration curves.
Use the drop-down menu or the keyboard Up/Down arrows to select each peak.
Click the Cancel button to return to the Calibration Setup. Click Cancel again to
return to the Interactive Graphics window.
Now you can display the Results Report for any run.
Click on the white chromatogram trace with the right mouse button. Select View
Results only.
The Verification Report for VERIF_3.RUN appears. Note that Peaks 4 and 9 are
marked as “Out of Verification Tolerance”.

Using the right mouse button, click anywhere on the light blue plot trace of the
sixth chromatogram, ANALYSIS.RUN. Select View Results Only.
Note the internal standard assignments listed for each peak and the standard
amounts documented below the listing of peaks results.
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Using the Calibration Curve Options (Curve Manager)

The window which displays the curves and curve options is called the Curve
Manager. This step lets you examine the features of some of these options. The
following steps will also allow processing of the set of data generated using the
Calibrating With External Standards tutorial. Screens and results will be similar.
Change the Sample Type of VERIF_3.RUN to Calibration and the Cal. Level to 3.
Deselect the Run DH check boxes for all data files except VERIF_3.RUN.
Select the Incorporate New Calibrations into Data Set option and press
Calculate Results.
After processing has completed, the data from VERIF_3.RUN will have been
added to the previous calibration set. All curves will now show two replicates for
level 3.
Select the menu command Results >View Calibration Curves... to view the
added data point. Display the curve for peak 9, n-Tridecane.
Select the Curve Only check box. Click on the Overlay button. Using the buttons
in the Overlay window below the Calibration Curve window, select
Quadratic>Ignore for Overlay Curve 1 and Cubic >Ignore for Overlay Curve 2.
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Choose to save the first fit by clicking on Save 1.

Select the X,Y cursor check box and then move the cursor along the calibration
curve.
Note the continuous readout of X and Y values. When you are finished, deselect
the X,Y cursor check box.
Position the cursor in the upper right corner of the graph and, with the left mouse
button, click and drag the cursor to a point below the single point as shown in the
next figure.
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Note that the area highlighted has been magnified and a small window showing
the entire graph has been displayed in the upper left corner of the display.
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You may continue zooming many times if you wish. At any time you may restore
the curve to full scale by clicking on the Full Scale button.
Click on the Full Scale button that appeared after you zoomed (see the lower left
corner of the plot area in the figure above).
Click on the X <--> Y... button and enter a value of 0.3 in the Amount field and
then click on Calculate.
The corresponding Peak Size (PS/PS Std.) is calculated determined by the

curve. Enter 1.0 in the Peak Size field and calculate the Amount (Amt./Amt. Std.)
determined by the curve.
Choose Cancel after you are done and deselect the Curve Only box to show the
header information.
Double-click on any point on the curve. The Point Info window appears. See the
figure next.
You may also access this window by clicking on the Point Info button above the
displayed curve.
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Various data file information is displayed for that point. You can view information
for all the points by using the Level/ Replicate arrows or by clicking on the
Next/Previous buttons.
Select the point at Level 3, Replicate 2 and exclude this point from the curve fit
calculations. Check the Exclude Selected Point from Calculation box.
This removes the point from the curve calculations and a new set of coefficients
is determined as shown in the next figure.
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Deselect the Exclude Selected Point from Calculation check box and close
the Point Info window by clicking on OK.
Click on the Coefficients button. In the Coefficients window (next figure),
change one of the coefficients by a small amount.
Click on the Overlay button in the Coefficients window to compare curves for
the two sets of coefficients.
Note that the header information displayed at the top of the Curve Manager
window indicates 'Edited' after fields that you modified during this tutorial. See
the following figure.
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Close the Calibration Curve window and exit the Interactive Graphics
application.
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2000 GC/MS Application Notes and
Advantage Notes
The following tables list Application Notes and Advantage Notes for the
2000 GC/MS. Copies of these notes are available through your Varian Sales
Representative. If you have Internet access, you may use your web browser to
examine these notes at:
http://www.varianinc.com
Application Note Index
Note Title/Description
1 Meeting Mass Spectral Tuning Criteria for EPA Environmental Methodology
Key Words: BFB, DFTPP, Tuning, Criteria;
2 Compound Verification and Spectral Integrity Over a Wide Concentration Range
with the Varian 2000 GC/MS
Key Words: Aldrin, Quadrupole, Linearity, Trace Analysis, Ion Trap
3 The Determination of Semivolatile Organic Compounds in Drinking Water by
EPA Method 525 with the Varian 2000 GC/MS
Key Words: Drinking Water, Method 525, Empore™, Semivolatiles, Pesticides
4 Tuning the Varian 2000 GC/MS to the EPA Method 625 DFTPP Criteria
Key Words: EPA Method 625, DFTPP, Tuning, Semivolatiles
5 2000 GC/MS System Minimizes Spectral Skew
Key Words: Spectral Skewing, DFTPP
6 New Generation Ion Trap GC/MS Technology Axial Modulation
Key Words: Axial Modulation, Mass Resolution, Sensitivity, Linearity
7 Polychlorinated Biphenyl Analysis and Complex Matrices
Key Words: Full Scale Information, Effluent Splitting, High Level Contamination,
Coal Tar
8 Determination of Volatile Organic Compounds in Water with the 2000 GC/MS;
Key Words: VOCs, Waste Water, Drinking Water, Purge and Trap, Direct
Interface
9 Use of the 2000 GC/MS Data System to Separate and Identify Multiple
Components in Reconstructed Total Ion Current Chromatographic Peaks
Key Words: Coelution, Peak Find Option, Maximized Mass, Biller-Bieman
Algorithm, Purge & Trap, Purgeable Organics
10 The Determination of Polyaromatic Hydrocarbons
221 of 225
Key Words: PAH (Polyaromatic Hydrocarbon), Complex Matrix, Ion Trap, PNA
(Polynuclear Aromatic), SPI Injector
11 Narrow Mass Range Scanning Versus Selected Ion Monitoring
Key Words: Selected Ion Monitoring, Narrow Mass Range, Enhanced
Sensitivity
12 The Determination of Triazine Herbicides at Ultra Trace Levels by Chemical
Ionization GC/MS
Key Words: Chemical Ionization, Herbicides, Automatic Reaction Control,
Isobutane, Molecular Weight Information
13 The Determination of Base/Neutrals in Extracts from Environmental Matrices
Key Words: Base/Neutrals, Full Scan, Coelutions, Inert Chromatography
14 The Determination of Phenols in Extracts from Environmental Matrices
Key Words: Phenols, Full Scan, Fast Inert Chromatography, Non-target
Compounds
15 The Determination of Acid/Base/Neutrals in an Industrial Effluent
Key Words: Base Neutrals, Complex Matrix, Ion Clusters
16 Determination of EPA Methods 524.2, 624 and 8260 Analytes with an Open
Split Interface to the 2000 GC/MS
Key Words: VOC, Purge and Trap, Open Split Interface, EPA Methods 525.2,
624 and 8260
17 Determination of Semivolatile Analytes by US EPA Method 8270 with the 2000
GC/MS;
Key Words: Semivolatiles, EPA Method 8270, Split Injection, Waste, Soils,
CLP Forms
18 The Determination of Volatile Organic Compounds (VOCs) in Air by the TO-14
Method Using the 2000 II GC/MS;
Key Words: VOCs, Air, Method TO-14, Cryotrapping, Full Scan Spectra
19 Direct Split Interface for Analysis of Volatile Organic Compounds
Key Words: Direct Split Interface, Non-Cryogenic Method, Purge and Trap,
VOC
20 Ozone Precursor Measurements in Ambient Air with the 2000 GC/MS;
Key Words: Air, VOCs, Hydrocarbons, Cryotrapping, Full Scan Spectra
21 Ultra Trace Analysis Using Selected Ion Storage GC/MS
Key Words: SIS, 2000, GC/MS, Pesticide, SPI, Wave~Board
22 Pesticide Residue Analysis of Bell Pepper Using Selection Ion Storage GC/MS
Key Words: Selected Ion Storage, SIS, Pesticide, SPI, 2000
23 Determination of Benzodiazepines in Human Blood Using Wave~Board
Technologies of the 2000 3 GC/MS
Key Words: Wave~Board, Blood, Diazepam, Nordiazepam, SECI, Drugs
24 Identification of a Fungicide Pollutant at Ultra Trace Levels by Ion Trap GC/MS
Key Words: Procymidone, Fungicide, Pesticide, Narrow Mass Range (NMR),
Wine, Pesticide Library, SPI
25 The Use of RF Storage Level for Background Elimination with the 2000 GC/MS
Key Words: RF Storage Voltage, Pate, Matrix Elimination, Pesticide, 2000
26 Screening for Pesticides in Food with the 2000 GC/MS
Key Words: Pesticide, 2000, RF Storage
222 of 225
Application Note Index
27 GC/MS/MS with a Benchtop Mass Spectrometer
Key Words: 2000 4D, MS/MS, Triple Quad, Timing Diagram
28 GC/MS/MS Analysis of Residual Pesticides in Vegetable Extracts
Key Words: 2000 4D, MS/MS, Pesticide, Wave~Board
29 Improved Detection Limits for PCBs in Transformer Oil by Increasing the RF
Storage Voltage
Key Words: PCBs, Transformer Oil, RF Storage Voltage, Ion Stability,
Ionization Time, Improved Detection Limits
30 GC/MS/MS Analysis of Thiabendazole in Grapefruit Extracts
Key Words: 2000 4D, MS/MS, Pesticide, Wave~Board
31 GC/MS Analysis of Organotin Compounds in the Environment
Key Words: 2000, Organotin, Environmental, Derivative
32 Determination of Polychlorinated Dibenz-p-dioxins and Dibenzofurans in
Environmental Samples with the 2000 GC/MS
33 GC/MS for the Detection of Illegal Use of Steroids in the Cattle Industry
Key Words: 2000, Steroids, 4-chlorotestosterone, Metabolites
34 Simultaneous Automated Spectral Screening and Quantitation of Picogram
Levels of Drugs
Key Words: Drug Analysis, THC, Benzodiazepines, Basic Drugs
35 Rapid Simultaneous Quantitation of Triazines, Organophosphates and PAHs
Key Words: Triazines, Organophosphates, PAHs, AGC
36 GC/MS/MS Analysis for the Identification of Impurities in Pharmaceutical
Products
Key Words: 2000 4D, GC/MS/MS, Pharmaceutical
37 The Determination of Trace Level FAMES Using CI Mode GC/MS
Key Words: FAMES, Fatty Acids, CI, Isobutane, SPI
38 Analysis of Estrogens in Sheep Liver Extracts Using Selected Ion Storage(SIS)
Key Words: Selected Ion Storage, Narrow Mass Range, High Background,
Estrogens
39 Quantitation of a Novel Cholinesterase Inhibitor in Human Plasma by GC/MS
Key Words: GC/MS, 2000, Cognition Activator, Human Plasma, Cholinesterase
Inhibitor
40 GC/MS/MS Analysis for Pesticide Residues in Agricultural Products
Key Words: 2000 4D, GC/MS/MS, Pesticide Residues, Food Analysis
41 Reformulated Fuel Analysis by GC/MS: Total Aromatic Hydrocarbons
Key Words: 2000 GC/MS, Aromatic Hydrocarbons, Reformulated Fuels, Full
Scan Spectra
42 The Determination of Sulfur Gases in Point Source Emissions of a Pulp Mill
Key Words: 2000 GC/MS, Sulfur Gases, Emission, Full Scan Spectra
43 GC/MS/MS Analysis of Dinitroaniline Based Herbicides in Fish
Key Words: 2000, GC/MS/MS, Herbicides, Fish
44 GC/MS/MS Analysis of Alkylated Polycyclic Aromatic Hydrocarbons
Key Words: 2000, GC/MS/MS, PAHs, CI/MS/MS
45 GC/MS/MS Analysis of PAHs in Water Using Large Volume Injections
223 of 225
Key Words: GC/MS/MS, PAHs, 1078 Injector, Large Volume Injection
46 Determination of Estradiol in Blood by GC/MS/MS
Key Words: GC/MS/MS, Estrogen, Estradiol, Large Volume Injections, MS/MS
ToolKit, 1078 Injector
47 GC/MS/MS Analysis of Planar PCBs in Biota and Sediment
Key Words: 2000, GC/MS/MS, Planar PCBs
48 GC/MS Analysis for Unsaturated Fat Content in Animal Feed
Key Words: 2000, Unsaturated Fat, GC/MS, Food, FAMES
49 Analysis of Hydrolyzed Vegetable Protein for Chloropropandiols using Selected
Ion Storage
Key Words: Selected Ion Storage, Food, Chloropropandiols, GC/MS
50 A Quantitative Comparison of TSD and GC/MS/MS for Atrazine in Surface
Water
Key Words: Atrazine, TSD, GC/MS/MS, 2000, Environmental
51 GC/MS/MS Analysis of Triazine Herbicide Residues using Multiple Reaction
Monitoring
Key Words: 2000, GC/MS/MS, ToolKit, MRM, Triazine, Herbicides
52 GC/MS/MS Analysis of β-Damascenone in Rose Oil
Key Words: 2000, GC/MS/MS, Flavor and Fragrance, Essential Oils
53 Multi-residue Analysis of Organophosphorus Insecticides by Ion Trap
GC/MS/MS
Key Words: 2000, MS/MS, Pesticides, Organophosphates
54 Enhanced Selectivity in the Determination of Triazines by Benchtop GC/MS/MS
Key Words: 2000, GC/MS/MS, Triazines, Environmental
55 GC/MS/MS Analysis of Cytostatic Drugs in Urine
Key Words: Toxicology, Clinical, Drugs
56 Rapid Analysis of Soils for Hazardous Waste by Direct Sample Introduction;
Key Words: 2000, Direct Sampling, ChromatoProbe, Herbicides, Soils
57 Chemical Ionization GC/MS for the analysis of Tributyltin Oxide
Key Words: TBTO, CI, Environmental 2000
58 App Note 58: Identification of Essential Oil Components EI/MS and Mixed
Reagent CI/MS
Key Words: Essential Oils, Flavors & Fragrances, Acetonitrile, CI
59 App Note 59: GC/MS Analysis for Morphine and Other Opiates in Urine
Key Words: Opiates, Urine, Drugs, 2000
60 GC/MS/MS Analysis for Anabolic Steroids in Urine for Athletic Testing
Key Words: Drugs, MS/MS
61 Chlorophenols in Drinking Water using GC/MS/MS
Key Words: MS/MS, Water, Phenols, EPA, Environmental
62 App Note 62: Detection of Gasoline in Fire Debris by GC/MS/MS
Key Words: MS/MS, Gasoline, Arson, Forensic
63 App Note 63: Tandem-in-Time Mass Spectrometry as a Quantitative
Bioanalytical Tool
Key Words: MS/MS, 2000
224 of 225
Advantage Note Index
Advantage Note Index
Note Title / Key Words

1 Advantages of New CI
Key Words: New CI Wave~Board, SECI
2 Advantage of CI, A Real Reason to Buy the SECI Option for the 2000 GC/MS;
Key Words: SECI, 2000
3 GC/MS/MS Analysis for Target Analytes in a Complex Matrix, Increased
Selectivity and Simplified Spectral Interpretation through GC/MS;
Key Words: MS/MS, Target Analysis, Alachlor, Pesticide, Complex Matrix,
Selectivity
4 GC/MS/MS Analysis for Unknown Compounds, Additional Information About
Key MS Fragments for Reconstruction of Structure and Studies of
Fragmentation Pathways;
Key Words: MS/MS, Qualitative Identification, Malathion, Pesticide,
Fragmentation Pathway
5 GC/MS/MS Analysis as a Separations Technique;
Key Words: GC/MS/MS, Coelution, Pesticide, MS/MS Separation
6 Multiple CI Gas Capability Enhances Flexibility of Ion Trap GC/MS;
Key Words: CI, Reagent Gas, SECI, Programmed Acquisition, External Events
7 GC/MS/MS Using Deuterated Internal Standard;
Key Words: GC/MS/MS Deuterated Internal Standard, Drugs
8 GC/MS/MS for Isomer Identification;
Key Words: GC/MS/MS, Isomer Identification, Pesticide
9 Hydrocarbon Identification Using the 2000 3 GC/MS;
Key Words: Hydrocarbon Identification, 2000, Industrial Application
10 Large Volume Injections for GC and GC/MS Analysis
Key Words: GC/MS/MS, 1078 Injector, Large Volume Injection
11 Maximize Information by Splitting Between the Ion Trap Mass Spec and a GC
Detector
Key Words: Splitter, 2000, GC, Detectors
12 Adv. Note 12: Enhanced Chromatographic Performance with a New Inert
Coating for the 2000 Ion Trap
Key Words: 2000, SilChrom, Drugs
13 Adv. Note 13: Confirmatory Analysis of Melatonin by EI and CI;
Key Words: 2000, CI, Drugs
14 Adv. Note 14: ChromatoProbe - A Simplified Approach to Sample Introduction
Key Words: 2000, Drugs, Direct Sampling, ChromatoProbe
15 Enhanced Molecular Weight Confirmation with Deuterated Acetonitrile CI
Key Words: LCI, Acetonitrile, FAMEs
16 Confirmation of Saturated Hydrocarbon Molecular Weight with Acetonitrile and
d3-Acetonitrile CI
Key Words: LCI, Acetonitrile, Hydrocarbons
225 of 225

Manual Workstation

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NOTICE: Varian, Inc.

was acquired by Agilent

©Varian, Inc. 2003-2006 Printed in U.S.A. 03-914988-00:Rev. 3

Acquiring a 2000 MS Data File...............................................................................................35

Quantitative Analysis of GC/MS Data ...................................................................................79

SIS and MS/MS Acquisitions ...............................................................................................127

Run File Tutorials .................................................................................................................145

Tutorial 1 Recalculating Results ........................................................................................147

Tutorial 2 Changing Peak Detection Parameters..............................................................161

Tutorial 3 Filling a Peak Table ............................................................................................173

Tutorial 4 Identifying Peaks ................................................................................................179

Tutorial 5 Using the II, SR, and VB Time Events ...............................................................185

Tutorial 6 Calibrating with an External Standard ..............................................................199

Tutorial 7 Calibrating with Internal Standards ..................................................................207

Running an MS Method without a GC Method

Loading an MS File in MS Data Review

Chromatogram and Spectra button on the MS Data Review toolbar. The

also be shown/hidden by clicking the Tree button in the MS Data Review

Select a data file and a descriptor to display a chromatogram. For example, to

You can also display Chromatograms by selecting File >Select Chromatogram

Data to Plot in the MS Data Review menu or the toolbar button.

Opening an MS File from Windows Explorer

Displaying Mass Chromatograms

File/Chromatogram.. in the MS Data Review menu or the toolbar button,

Displaying Multiple Chromatograms

5. Select the “p” button to sort the displayed chromatograms by Plot

6. Use the toolbar button in the Plot Chromatograms and Spectra

File >Select File/Chromatogram in the MS Data Review menu or the

Getting Spectra from an MS file

Performing a Background Correction

Use the command Chromatogram >Edit Background Correction… to enter

You may also use the toolbar button .

Performing a NIST Library Search

After a spectrum of interest is displayed, press the Search toolbar button

searched spectrum. Press the button and select Spectrum Search.

How to Create or Edit NIST libraries

Building a Spectrum List

2. In the MS Data Review menu select Chromatogram >Set Single Click

spectra by using the Delete Spectrum button .

To edit an attribute (name, comment, formula, molecular weight, CAS number,

Creating and Using a Spooler File

2. Select File >Send Reports to Spooler File.

Click on the Export Chromatograms and Spectra button in the MS Data

A graphical representation of the acquisition segments is displayed at the bottom

Starting the Varian MS Workstation

Setting Instrument Configuration for Manual Injections

Running an MS Method without a GC Method

Adjusting and Tuning the 2000

Adjusting Calibration Gas

Choosing Auto Tune Methods

Required Frequency of Tuning

NOTE: The RF voltage ramp should be checked and adjusted, if needed,

Examining Current Module Attributes

Creating a New Method

Choose Instrument 1 and click Next in the Select Configuration window.

If the GC was removed from the instrument, it won’t be displayed as part of

NOTE: The MS Data Handling section would be added to perform post-run

Examine the parameters which may be adjusted in the Segment Setpoints

Starting the Acquisition

Activating the GC/MS Method