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2000 GC-MS
Operation Manual
597 pgs4.86 Mb0
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Varian 2000 GC-MS Operation Manual

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 This document is provided as a courtesy but is no longer kept current and thus will contain historical references to Varian.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 information, go to www.agilent.com/chem.
Varian, Inc. 2700 Mitchell Drive Walnut Creek, CA 94598-1675/USA
Saturn® 2000 GC/MS
MS Workstation
Operation Manual
©Varian, Inc. 2003-2009 Printed in U.S.A. 03-914979-00:5

Contents

Getting Started........................................................................................................................11
About this Manual/Help ............................................................................................................................................11
Additional Manuals/Help...........................................................................................................................................11
MS Workstation Toolbar ........................................................................................................13
Overview...................................................................................................................................................................13
Elements of the MS Workstation Toolbar.................................................................................................................14
Launching Applications from the MS Workstation Toolbar
Using the Application Icon Buttons...........................................................................................................................19
Using the Data File and Method Quick Link buttons................................................................................................19
................................................19
MS Workstation Toolbar Options..........................................................................................21
Moving the MS Workstation Toolbar........................................................................................................................21
The MS Workstation Toolbar Options Menu............................................................................................................21
2000 MS Module Control........................................................................................................25
Starting System Control the First Time ....................................................................................................................25
Configuring the Instrument.......................................................................................................................................25
Configuring the 3800 or 3900 GC Communication (No Company Network) ...........................................................32
Configuring the GC for a Company Network............................................................................................................34
Using a Password to Protect BOOTP Settings ........................................................................................................39
Adding a GC and Varian MS to the Instrument in System Control ..........................................................................41
2000 MS Instrument Control Command Reference
Saturn Module Dialogs.............................................................................................................................................47
2000 Module Window...............................................................................................................................................48
2000 MS Instrument Window
The 2000 MS Instrument Window............................................................................................................................59
Status and Control Window......................................................................................................................................73
.................................................................................................59
.............................................................47
3800 GC System Control Window.........................................................................................99
The Instrument Window............................................................................................................................................99
The 3800 GC Status and Control Window.............................................................................................................100
Documenting Module Information ..........................................................................................................................104
3800 GC Injecting a Single Sample.....................................................................................107
Overview.................................................................................................................................................................107
Using the Inject Single Sample Dialog Box............................................................................................................107
Specifying the Data File Name and Path ...............................................................................................................108
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Specifying Per-Sample Data Handling Parameters ...............................................................................................109
Specifying a RecalcList ..........................................................................................................................................110
Monitoring the Status of the Run............................................................................................................................110
Using QuickStart.....................................................................................................................................................111
3800 GC Injecting Multiple Samples ...................................................................................113
Introduction.............................................................................................................................................................113
Using a SampleList in System Control...................................................................................................................113
Specifying the Data File Name and Path ...............................................................................................................115
Specifying Per-Sample Data Handling Parameters ...............................................................................................116
Specifying a RecalcList ..........................................................................................................................................116
Changing Default SampleList Entries.....................................................................................................................117
Reading Vial Positions from an 8200 AutoSampler ...............................................................................................117
Monitoring the Status of Runs................................................................................................................................118
Saving SampleLists for Later Use..........................................................................................................................119
Using More Than One Method for Injections..........................................................................................................119
3900 GC System Control Window.......................................................................................123
The Instrument Window..........................................................................................................................................123
The 3900 GC Status and Control Window.............................................................................................................124
Documenting Module Information ..........................................................................................................................128
3900 GC Injecting a Single Sample.....................................................................................131
Overview.................................................................................................................................................................131
Using the Inject Single Sample Dialog Box............................................................................................................131
Specifying the Data File Name and Path ...............................................................................................................132
Specifying Per-Sample Data Handling Parameters ...............................................................................................132
Specifying a RecalcList ..........................................................................................................................................133
Monitoring the Status of the Run............................................................................................................................133
Using QuickStart.....................................................................................................................................................134
3900 GC Injecting Multiple Samples ...................................................................................137
Introduction.............................................................................................................................................................137
Using a SampleList in System Control...................................................................................................................137
Specifying the Data File Name and Path ...............................................................................................................139
Specifying Per-Sample Data Handling Parameters ...............................................................................................140
Specifying a RecalcList ..........................................................................................................................................140
Changing Default SampleList Entries.....................................................................................................................141
Monitoring the Status of Runs................................................................................................................................141
Saving SampleLists for Later Use..........................................................................................................................142
Using More Than One Method for Injections..........................................................................................................142
System Control Menus.........................................................................................................145
File Menu................................................................................................................................................................145
Edit Menu................................................................................................................................................................146
Inject Menu.............................................................................................................................................................147
Automation Menu....................................................................................................................................................147
Recalculate Menu...................................................................................................................................................148
Instrument Menu.....................................................................................................................................................148
Windows Menu.......................................................................................................................................................149
Help Menu ..............................................................................................................................................................150
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System Control Toolbar.......................................................................................................151
Main Toolbar...........................................................................................................................................................151
2000 MS Method Basic Scan Functions .............................................................................153
Introduction.............................................................................................................................................................153
2000 MS Method Chemical Ionization.................................................................................155
Introduction.............................................................................................................................................................155
The Chemical Ionization Scan Function.................................................................................................................155
Ion Formation By Chemical Ionization....................................................................................................................157
The CI Parameters .................................................................................................................................................158
Chemical Ionization Using Fixed Parameters ........................................................................................................162
Using Liquid CI Reagents.......................................................................................................................................162
Adjusting the CI Reagent Gas Pressure for Gases Other Than Methane.............................................................165
Tuning for CI Operation..........................................................................................................................................166
Low-Pressure CI vs. High Pressure CI...................................................................................................................166
Recommended Reading.........................................................................................................................................167
2000 MS Method Command Reference...............................................................................169
Spreadsheet editing................................................................................................................................................169
The CI Parameters .................................................................................................................................................175
CI Fixed Parameters...............................................................................................................................................176
Ion Storage (SIS) Parameters................................................................................................................................177
Customize SIS........................................................................................................................................................177
The MS/MS Ion Prep Method.................................................................................................................................178
The MS “q” Calculator ............................................................................................................................................178
Ion Preparation MS/MS..........................................................................................................................................183
MSn.........................................................................................................................................................................185
2000 MS Method Electron Ionization ..................................................................................189
The Electron Ionization Scan Function with Automatic Gain Control (AGC) .........................................................189
Ion Formation..........................................................................................................................................................190
AGC Prescan..........................................................................................................................................................190
Mass Scanning.......................................................................................................................................................191
Basic Equation of the AGC Software .....................................................................................................................192
Software Parameters..............................................................................................................................................193
2000 MS Method Ion Preparation
The Ion Preparation Method...................................................................................................................................199
Theory of Operation of the SIS Option...................................................................................................................201
Selected Ion Storage (SIS) Parameters.................................................................................................................202
Customize SIS........................................................................................................................................................203
Tips for Using SIS...................................................................................................................................................205
The MS “q” Calculator ............................................................................................................................................205
........................................................................................199
2000 MS Method MS/MS Option: Theory of Operation.....................................................207
Overview.................................................................................................................................................................207
The MS/MS Ion Prep Method.................................................................................................................................212
The MS “q” Calculator ............................................................................................................................................214
Customize Non-resonant Method...........................................................................................................................214
Customize Resonant Method................................................................................................................................217
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Tandem Mass Spectrometry (MS/MS)...................................................................................................................219
Automated Methods Development.........................................................................................................................221
MS/MS....................................................................................................................................................................224
Unit Resolution Selected Ion Storage ....................................................................................................................224
MS/MS/MS..............................................................................................................................................................224
2000 MS Method Section......................................................................................................227
Overview.................................................................................................................................................................227
Using Star Assistant to Create a New Method.......................................................................................................227
The Method Builder Window ..................................................................................................................................230
The 2000 MS Method Windows .............................................................................................................................231
The Flow Sampling Segment .................................................................................................................................233
2000 MS Method System Control
The Startup Method................................................................................................................................................235
Editing Methods from the Saturn Status and Control Window...............................................................................236
Changing Method End Time from the Saturn Control and Status Window............................................................236
Importing Method Sections.....................................................................................................................................237
Deleting Method Sections.......................................................................................................................................238
Printing the Method ................................................................................................................................................239
Password Protecting a Method ..............................................................................................................................239
........................................................................................235
3800 GC Method Command Reference...............................................................................241
3800 GC AutoSampler ...........................................................................................................................................241
3800 GC Sample Delivery......................................................................................................................................248
3800 GC Injector ....................................................................................................................................................249
3800 GC Flow/Pressure.........................................................................................................................................253
3800 GC Column Oven..........................................................................................................................................256
3800 GC Detector...................................................................................................................................................257
3800 GC Output......................................................................................................................................................265
3800 GC Data Acquisition......................................................................................................................................266
3800 GC Method Section......................................................................................................267
Overview.................................................................................................................................................................267
Using Star Assistant to Create a New Method.......................................................................................................267
The Method Builder Window ..................................................................................................................................270
The 3800 GC Method Windows .............................................................................................................................271
Sample Delivery Window........................................................................................................................................274
Injector Window......................................................................................................................................................276
Flow/Pressure Window...........................................................................................................................................281
Column Oven Window............................................................................................................................................285
Detector Window ....................................................................................................................................................286
Output Window.......................................................................................................................................................294
Data Acquisition Window........................................................................................................................................295
Autosampler Window..............................................................................................................................................296
Auto-Configuring the Method to Match the 3800 GC Hardware ............................................................................297
Uploading the Method from the 3800 GC...............................................................................................................297
The Startup Method................................................................................................................................................298
Editing Methods from the 3800 Status and Control Window..................................................................................298
Importing Method Sections.....................................................................................................................................299
Deleting Method Sections.......................................................................................................................................300
Printing the Method ................................................................................................................................................301
Password Protecting a Method ..............................................................................................................................301
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3800 GC System Control Command Reference.................................................................303
Status and Control Window....................................................................................................................................303
Setup Ethernet Ports Dialog Box............................................................................................................................327
8400/8410 SampleList Window Extensions...........................................................................................................330
3900 GC Method Command Reference
3900 GC AutoSampler ...........................................................................................................................................333
3900 GC Injector Section .......................................................................................................................................341
3900 GC Flow/Pressure Section............................................................................................................................343
3900 GC Column Oven Section.............................................................................................................................344
...............................................................................333
3900 GC Method Section......................................................................................................345
Overview.................................................................................................................................................................345
Using Star Assistant to Create a New Method.......................................................................................................345
The Method Builder Window ..................................................................................................................................348
The 3900 GC Method Windows .............................................................................................................................349
GC Control Window................................................................................................................................................352
Autosampler Window..............................................................................................................................................356
Auto-configuring the Method to Match the 3900 GC Hardware.............................................................................357
Uploading the Method from the 3900 GC...............................................................................................................357
The Startup Method................................................................................................................................................358
Editing Methods from the 3900 Status and Control Window..................................................................................358
Importing Method Sections.....................................................................................................................................359
Deleting Method Sections.......................................................................................................................................360
Printing the Method ................................................................................................................................................362
Password Protecting a Method ..............................................................................................................................362
3900 GC System Control Command Reference.................................................................363
Status and Control Window....................................................................................................................................363
Setup Ethernet Ports Dialog Box............................................................................................................................377
8200 AutoSampler Instrument Control Command Reference .......................................... 381
8200 AutoSampler Status and Control Window.....................................................................................................381
8200 SampleList Window Extensions....................................................................................................................385
8200 Method Command Reference
8200 Configuration Window ...................................................................................................................................389
Automated MS Report Generation
Overview.................................................................................................................................................................393
.....................................................................................389
......................................................................................393
Automation File Editor Command Reference ....................................................................395
Menus.....................................................................................................................................................................395
Main Toolbar...........................................................................................................................................................397
Open Automation File Dialog Box ..........................................................................................................................398
Save Automation File As Dialog Box......................................................................................................................399
Print Setup Dialog Box ...........................................................................................................................................400
Edit Notes Dialog Box.............................................................................................................................................401
RecalcList Window.................................................................................................................................................402
SampleList Window................................................................................................................................................408
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Sequence Window..................................................................................................................................................414
Automation File Editor.........................................................................................................415
Overview.................................................................................................................................................................415
Accessing the Automation File Editor.....................................................................................................................415
Editing or creating a RecalcList..............................................................................................................................415
Editing or creating a SampleList.............................................................................................................................417
Specifying the Data File Name and Path ...............................................................................................................419
Specifying Per-Sample Data Handling Parameters ...............................................................................................420
Specifying a RecalcList ..........................................................................................................................................421
Changing Default SampleList Entries.....................................................................................................................421
Using More Than One Method for Injections..........................................................................................................422
Editing or Creating a Sequence .............................................................................................................................423
GC Batch Report...................................................................................................................425
Overview.................................................................................................................................................................425
Method Selection....................................................................................................................................................426
Generating Reports................................................................................................................................................427
Changing Report Commands.................................................................................................................................427
GC Data Handling Calibration .............................................................................................429
Types of Calibration................................................................................................................................................429
Preparing the Method for Calibration .....................................................................................................................429
Automated Calibration............................................................................................................................................430
Inspecting Calibration Curves ................................................................................................................................431
Generating Calibration Block Reports....................................................................................................................433
Calibration Verification............................................................................................................................................434
GC Data Handling Fundamentals........................................................................................435
Introduction.............................................................................................................................................................435
Performing a Pilot Run ...........................................................................................................................................435
Peak Detection .......................................................................................................................................................436
Identifying Peaks ....................................................................................................................................................439
Building a Calibration Curve...................................................................................................................................439
External Standard Calibration.................................................................................................................................440
Internal Standard Calibration..................................................................................................................................441
Normalized Percent Calibration..............................................................................................................................441
Choosing a Calibration Type..................................................................................................................................441
GC Data Handling Method Command Reference
Integration Parameters...........................................................................................................................................443
Peak Table..............................................................................................................................................................445
Calibration Setup....................................................................................................................................................447
Calibration Curve Window......................................................................................................................................450
Verification Setup....................................................................................................................................................454
Time Events Table..................................................................................................................................................455
...............................................................443
GC Interactive Graphics Dialog Boxes...............................................................................459
Open Multiple Data Files Dialog Box......................................................................................................................459
Open Method File Dialog Box.................................................................................................................................462
Open Original/Recalc Dialog Boxes.......................................................................................................................463
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Save Method As Dialog Box...................................................................................................................................464
Saturn Printer Setup Dialog Box.............................................................................................................................465
Preferences Dialog Box..........................................................................................................................................465
Reintegration List Dialog Box.................................................................................................................................471
Fill Peak Table Window..........................................................................................................................................473
Exact View Dialog Box ...........................................................................................................................................474
GC Interactive Graphics Menus ..........................................................................................475
File Menu................................................................................................................................................................475
Edit Menu................................................................................................................................................................476
View Menu..............................................................................................................................................................476
Results Menu..........................................................................................................................................................477
Edit Method Menu...................................................................................................................................................478
Help Menu ..............................................................................................................................................................479
GC Interactive Graphics Toolbars.......................................................................................481
Toolbar Overview ...................................................................................................................................................481
Main Toolbar...........................................................................................................................................................481
Method Quick Link Toolbar.....................................................................................................................................482
Chromatogram Toolbar ..........................................................................................................................................482
GC Interactive Graphics Window........................................................................................485
Locator Window......................................................................................................................................................485
Main Window..........................................................................................................................................................486
Info-Panels..............................................................................................................................................................489
Visual Method Edit Window....................................................................................................................................491
GC Interactive Graphics .......................................................................................................497
Viewing Chromatograms in Interactive Graphics...................................................................................................497
Elements of the Interactive Graphics Window........................................................................................................498
Changing Viewing Options.....................................................................................................................................501
Selecting a Method.................................................................................................................................................504
Changing the Data Handling Parameters...............................................................................................................507
Filling the Peak Table.............................................................................................................................................510
Interactive Editing of Timed Events........................................................................................................................511
Moving Peak Start and End Points.........................................................................................................................513
Calculating Results.................................................................................................................................................513
Viewing Results......................................................................................................................................................515
Viewing Calibration Curves ....................................................................................................................................516
Printing and Copying the Chromatogram Display..................................................................................................517
GC Standard Report Method Command Reference
Print Options...........................................................................................................................................................519
Results Format .......................................................................................................................................................521
Chromatogram Format...........................................................................................................................................522
Calibration Block Report Format ............................................................................................................................524
...........................................................519
Generating GC Standard Reports .......................................................................................525
The Standard GC Reports Method Section............................................................................................................525
Automated Report Generation................................................................................................................................528
Automated Printing to Multiple Printers..................................................................................................................529
7
Batch Report Printing without Recalculating..........................................................................................................530
Viewing a Report for a Single Run .........................................................................................................................531
Method Builder Dialog Boxes..............................................................................................535
Create/Open Method File Dialog Box.....................................................................................................................535
Open Method File Dialog Box.................................................................................................................................536
Save Method File As Dialog Box............................................................................................................................537
Add Password Dialog Box......................................................................................................................................538
Change Password Dialog Box................................................................................................................................539
Print Method Sections Dialog Box..........................................................................................................................540
Star Printer Setup Dialog Box.................................................................................................................................541
Delete Method Sections Dialog Box.......................................................................................................................542
Import Method File Sections Dialog Box................................................................................................................543
Star Assistant Wizard .............................................................................................................................................543
Method Builder Menus.........................................................................................................549
File Menu................................................................................................................................................................549
Edit Menu................................................................................................................................................................550
View Menu..............................................................................................................................................................550
Window Menu.........................................................................................................................................................550
Help Menu ..............................................................................................................................................................551
Method Builder Toolbars .....................................................................................................553
Overview.................................................................................................................................................................553
Main Toolbar...........................................................................................................................................................553
Directory Toolbar....................................................................................................................................................554
Window Toolbar......................................................................................................................................................555
Method Builder Window.......................................................................................................557
Overview.................................................................................................................................................................557
Method Directory ....................................................................................................................................................558
Method Parameters................................................................................................................................................559
Module Information Editor...................................................................................................561
Module Information Editor ......................................................................................................................................561
Creating a Section..................................................................................................................................................562
Deleting a Section ..................................................................................................................................................562
Renaming a Section...............................................................................................................................................562
Adding an Entry to a Section..................................................................................................................................563
Deleting an Entry from a Section............................................................................................................................563
Editing an Entry or Renaming an Item ...................................................................................................................563
Creating a Default Module Information Template ..................................................................................................564
Designing Documentation Structures.....................................................................................................................564
Retrieving Information from Data Files...................................................................................................................565
Commands .............................................................................................................................................................565
Dialog Boxes...........................................................................................................................................................566
Security Administration.......................................................................................................569
Overview.................................................................................................................................................................569
Passwords..............................................................................................................................................................569
Application Locking.................................................................................................................................................571
8
File Revision Settings.............................................................................................................................................572
Standard GC Reports Command Reference ......................................................................575
File Menu................................................................................................................................................................575
Search Menu ..........................................................................................................................................................575
Font Menu...............................................................................................................................................................575
View Menu..............................................................................................................................................................576
Options Menu .........................................................................................................................................................576
Windows Menu.......................................................................................................................................................576
Help Menu ..............................................................................................................................................................577
Standard GC Reports Dialog Boxes....................................................................................579
Open Data File Dialog Box.....................................................................................................................................579
Print Dialog Box......................................................................................................................................................580
Printer Setup Dialog Box........................................................................................................................................581
Title Dialog Box.......................................................................................................................................................581
Chromatogram Options Dialog Box........................................................................................................................582
Results Options Dialog Box....................................................................................................................................584
Find Dialog Box ......................................................................................................................................................585
Standard GC Reports Format Descriptions .......................................................................587
Results Report........................................................................................................................................................587
Verification Report..................................................................................................................................................593
Standard GC Reports Toolbar.............................................................................................595
Main Toolbar...........................................................................................................................................................595
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10

Getting Started

About this Manual/Help

This manual/help system contains information about how to acquire data, build methods, and operate the Saturn GC/MS through the Varian MS Workstation. This manual also describes the configuration of the 3800 and 3900 GCs for standard Ethernet communication with the Saturn 2000 and MS Workstation’s System Control application. Use this manual in conjunction with the other manuals supplied with your MS Workstation and your 3800 GC or 3900 GC. All of the information included in this manual is also available in the On-Line Help section of the software.

Additional Manuals/Help

Other sources of information are available to help you get the most from this product.

2000 GC/MS Hardware Reference Manual/Help

The Hardware Reference Manual/Help system provides the necessary information for installing, maintaining, using and repairing your Saturn GC/MS System. All of the information included in this manual is also available in the On­Line Help section of the software.

MS Workstation Manual/Help

This Manual/Help provide a practical way to quickly learn how to perform basic tasks using the MS Workstation Software. While these tutorials use Saturn 2000 ion trap files, they can easily be adapted to your instrument configuration.

3800 and 3900 GC Operator’s Manuals

These manuals are included on the Varian MS Workstation CD-ROM and describe the GC Method, instrument operation, and the process of connecting your GC to a PC or to an existing network.

Context Sensitive Help

The MS Data Review, Method Builder and System Control sections of the software contain Context Sensitive Help. Help can be obtained simply by positioning the mouse pointer on the item of interest, clicking the right mouse button and selecting "What's This".
11
12

MS Workstation Toolbar

Overview

Saturn GC/MS Workstation is a suite of applications for controlling chromatographs, collecting data from chromatograph detectors, and analyzing those data. The MS Workstation Toolbar provides quick and easy access to the Saturn GC/MS Workstation applications. When activated, the MS Workstation Toolbar behaves very much like the Windows Taskbar. It can be docked on any of the four sides of the display screen and other Windows programs will not cover or go behind it when they are opened in full screen mode.
If the MS Workstation Toolbar is not already opened on your Saturn GC/MS Workstation, you can start it from the Windows Start Menu.
13

Elements of the MS Workstation Toolbar

Application Buttons for immediate access to the selected application.
Tooltip shows the application name when the cursor rests on the Application Button.
Quick Link Buttons provide menu selections of operations to be performed on the listed file.
Application Descriptions give a brief description of the application that will be opened when the cursor rests on the Application Button.
14

Application Buttons

Used to monitor instrument status, perform automated injections, and perform batch recalculations.
Used to view and edit instrument operation, data acquisition, and data handling methods.
Used for off-line editing of SampleLists, RecalcLists and Sequences.
Used to review chromatograms and spectra, perform library searches, and review and process quantitation results.
Used to create, edit, and view standard MS reports.
Used to create, edit, and view customized MS reports.
Used to convert data files between DOS and Windows formats.
Used to review standard GC chromatograms, interactively edit data handling parameters, and recalculate results.
Used to preview standard chromatogram and results reports.
Used to generate standard reports for a group of Data Files by dragging and dropping them on the Batch Report Window.
Used to run a sample without a Sample List.
Used to set Saturn GC/MS Workstation security options and passwords.
In addition, other application buttons may be added to the MS Workstation Toolbar when you install additional Saturn GC/MS Workstation options, such as StarFinder and Star Custom Report Writer.
15

Quick Link Buttons

Most Recently Used Data File. A menu of operations that can be performed on the Most Recently Used Data File are displayed when the button is pressed. A different data file can be selected from a list of most recently used files.
Most Recently Used Method. Menu of operations that can be performed on the Most Recently Used Method will be displayed when the button is pressed. A different method can be selected from a list of most recently used methods.
16

MS Workstation Toolbar Options

Right-click the bar to display the Toolbar Options. A menu of MS Workstation Toolbar configuration options and operations that may be performed will be shown.
17
18

Launching Applications from the MS Workstation Toolbar

Using the Application Icon Buttons

Saturn GC/MS Workstation applications appear as icon buttons on the MS Workstation Toolbar. As you move the mouse over these buttons, the name of the application is shown in a tooltip window below the cursor.
Click any icon in the MS Workstation Toolbar to launch the corresponding application.

Using the Data File and Method Quick Link buttons

The two buttons to the right of the application buttons are Quick Link buttons. These two Quick Link buttons correspond to recently used Data Files and Methods. On each Quick Link button is the name of the file associated with that button. When you click the Quick Link button, a menu is displayed showing operations that can be performed on the corresponding file.
The Quick Link buttons in the MS Workstation Toolbar are always updated with the most recently used Data File and Method. If the Data File or Method you wish to use is not displayed in the Quick Link button, you can choose from the eight most recently used files by selecting “Pick a different Data File (or Method)” from Quick Link button’s menu.
19
20

MS Workstation Toolbar Options

Moving the MS Workstation Toolbar

The MS Workstation Toolbar can be moved to any edge of the Windows screen. Click a portion of the MS Workstation Toolbar that does not contain application or Quick Link buttons and drag the toolbar to the edge of the screen that you desire. When you release the mouse, the toolbar will remain on that edge. The MS Workstation Toolbar remembers its location the next time it is started.
Additionally, you can display the MS Workstation Toolbar as a Windows Taskbar icon. To do so, select “Move to Windows Taskbar” from the MS Workstation Toolbar options menu. Taskbar icons appear in the lower right (or bottom) of the Windows Taskbar (the bar on which the “Start” button appears). When displayed as a Taskbar icon, the toolbar no longer takes up space on the screen. When you click the MS Workstation Toolbar icon, the options menu is displayed.

The MS Workstation Toolbar Options Menu

When you move the mouse over an area of the MS Workstation Toolbar not containing application or QuickLink buttons, you may right-click to display an option menu.
21

Move to Windows Taskbar

You can display the MS Workstation Toolbar as a Windows Taskbar icon. Taskbar icons appear in the lower right (or bottom) of the Windows Taskbar (the bar on which the “Start” button appears). When displayed as a Taskbar icon, the toolbar no longer takes up space on the screen. When you click the MS Workstation Toolbar icon, the options menu is displayed.

Show/Hide Applications on Toolbar

Selecting this option displays the Show and Hide Applications on Toolbar dialog box.
This dialog box allows you to select which Saturn GC/MS Workstation applications are represented by icons on the MS Workstation Toolbar. The top list box shows all applications that are currently displayed in the toolbar. The bottom list shows all applications that are installed but not displayed in the toolbar. To remove an icon from the toolbar, select it from the top list and click Remove. To add an icon to the toolbar, select it from the bottom list and click Add.

Enable/Disable Instrument Modules

Selecting this option displays the Enable/Disable Instrument Modules dialog box.
22
This dialog box allows you to select which Saturn GC/MS Workstation instrument modules are available from this Workstation. When an instrument module is available, it will appear in System Control if the corresponding instrument is connected and powered-on, you will be able to create a Method section for it, and you will be able to format reports for it.
The top list box shows all instrument modules that are currently installed and enabled in the Saturn GC/MS Workstation. The bottom list shows all instrument modules that are installed but not enabled. To disable an instrument module, select it from the top list and click Disable. To enable an instrument module, select it from the bottom list and click Enable.

Application Descriptions

When this menu item is checked, application descriptions are displayed when you move the mouse over application buttons in the MS Workstation Toolbar.

Small Buttons on Toolbar

When this menu item is checked, the MS Workstation Toolbar is reduced in size.
23

Run Application

This hierarchical menu item lists all applications showing on the MS Workstation Toolbar. When you select an item from this list, the corresponding application is launched.

Help on

This hierarchical menu item lists all applications showing on the MS Workstation Toolbar. When you select an item from this list, the online help corresponding to the application is displayed.

Pick Data File for Quick Link Button

This hierarchical menu item lists the eight most recently used Data Files in order of use. When you select a Data File from this list, the Data File currently displayed in the Quick Link button is changed to the selected file.

Pick Method for Quick Link Button

This hierarchical menu item lists the eight most recently used Methods in order of use. When you select a Method from this list, the Method currently displayed in the Quick Link button is changed to the selected file.

Help on MS Workstation Toolbar

Displays the help you are now using.

Product Support Web Site

If you have Internet access and a web browser installed on your computer, this option will automatically open the Saturn GC/MS Workstation Product Support Web Site. Here you will find the latest software and documentation updates for the Saturn GC/MS Workstation suite of products, along with additional notes, tips, and answers to frequently asked questions.
You may wish to visit this site periodically to see if new information is available that may be pertinent to you.

About MS Workstation Toolbar

Displays the About Box for the MS Workstation Toolbar. The About Box contains information about the software version, installation information, and a list of the instrument control modules that you have installed.

Quit

Quits the MS Workstation Toolbar application. If you elected to run the MS Workstation Toolbar automatically when Windows starts, the MS Workstation Toolbar will reappear the next time you start Windows.
24

2000 MS Module Control

Starting System Control the First Time

Before you enter System Control for the first time, confirm that the proper instrument modules have been enabled and that any instrument modules that are not part of the system have been disabled. To enable or disable instrument modules refer to the section of the MS Workstation Toolbar, Enable/Disable Instrument Modules.

Configuring the Instrument

Before beginning the configuration process, you should know whether you will be attaching your Workstation and 3800 or 3900 GC to a company network or an isolated network only used for instrument control. If you have a Network Administrator on site, you may wish to ask which configuration is recommended.
Use this table to determine the order in which you should read the following sections.
1. If an Ethernet card has not been installed and configured on your PC, read Installing and Configuring the Ethernet Card in Your PC and one of the following:
No Company Network: Configuring TCP/IP Parameters with no
Company Network.
Company Network: Configuring TCP/IP Parameters for a Company Network.
2. Read Connecting Your 3800 or 3900 GC to Your PC or Network. If you have not already installed the Varian MS Workstation, do so before
3. proceeding.
No Company Network: Read Configuring the 3800 or 3900 GC
Communication (No Company Network). Company Network: Read Configuring the GC for a Company Network. Continue reading the rest of the sections, starting with Adding a GC and
4. Varian MS to the Instrument in System Control.
Installing and Configuring the Ethernet Card in Your PC.
5.
NOTE: The following section describes a procedure that is relatively generic; consult your Windows documentation and that of the Ethernet card’s manufacturer for more detailed explanations.
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Refer to the installation instructions packaged with your Ethernet card for information on installing the Ethernet card in your computer. Before proceeding, your Ethernet card should be recognized by your Windows version. When done, the Network Neighborhood icon should appear on your Windows desktop.
NOTE: For the following procedure, the use of disks other than the ones that were used for the original Windows installation may result in a Ethernet driver version mismatch that keeps Windows from starting. Should this occur, it may be necessary to remove the Ethernet Board from the computer to remove the incorrect Ethernet drivers.
You must configure your computer’s network settings to allow communication with the 3800 or 3900 GC. You do so by running the Windows Control Panel.
1. Run the Control Panel by selecting it from the Start menu (under Control Panel or Settings).
The Control Panel window is displayed.
2. Double-click the Network icon to set your Network options.
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The Network dialog box is displayed.
3. If TCP/IP is already listed in the list of network components, skip to the Note after step 5, otherwise, click Add.
The Select Network Component Type dialog box is displayed.
4. Select Protocol and click Add.
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The Select Network Protocol dialog box is displayed.
5. Select Microsoft as the manufacturer. Select TCP/IP as the protocol. Click OK. The protocol is added to your installed network Component list.
NOTE: If you are not connecting your Workstation to a company network (that is, you are not assigned an IP address by a Network Administrator), follow the next three steps. If you are connecting your Workstation to a company network, skip to Configuring the GC for a Company Network.

Configuring TCP/IP Parameters with no Company Network

The following three steps assume you have completed steps 1 through 5 from the previous procedure.
1. Select TCP/IP from the network components list and click Properties. The TCP/IP properties dialog box is displayed.
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