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11
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 On-
Line 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".
- Operation Manual 1
- Contents 3
- Getting Started 13
- MS Workstation Toolbar 15
- Button 16
- Application Buttons 17
- Quick Link Buttons 18
- Move to Windows Taskbar 24
- Application Descriptions 25
- Small Buttons on Toolbar 25
- 2000 MS Module Control 27
- Network 30
- Company Network) 34
- Server] 35
- Click Setup 35
- 2000 MS Instrument Control 49
- 2000 Module Window 50
- Manual Control 51
- Instrument Settings 52
- Setpoints tab 52
- Adjustments tab 52
- Auto Tune 53
- Set Points 54
- Temperatures 55
- Diagnostics Mode 55
- System Test 56
- Monitor Window 57
- Shutdown Mode 58
- Acquisition Mode 59
- 2000 MS Instrument Window 61
- Inject Single Sample Menu 64
- Saturn Module Keypad Dialog 71
- Spectrum Toolbar 72
- Status and Control Window 75
- Operating Conditions 77
- SetPoints 77
- Adjustments 78
- See the Chemical Ionization 81
- Autotune Mode 82
- Control and Status 83
- Method and Set Points 83
- Auto Tune Checks 85
- Air/Water Check 85
- Electron Multiplier Tune 86
- Mass Calibration 88
- Trap Function Calibration 89
- Temperatures Mode 90
- Diffusion Pump Shutdown 94
- Diffusion Pump Startup 95
- Acquisition 96
- Electron Multiplier Gain 98
- Axial Modulation 99
- Emission Current 99
- Ion Trap Temperature 99
- AGC Target TIC Value 100
- The Instrument Window 101
- Overview 109
- Specifying a RecalcList 112
- Using QuickStart 113
- 3800 GC Injecting Multiple 115
- Samples 115
- Using the Sequence Window 122
- Adjust time scale 130
- Select Edit Module Info 131
- 3900 GC Injecting Multiple 139
- System Control Menus 147
- Edit Menu 148
- Inject Menu 149
- Automation Menu 149
- Recalculate Menu 150
- Instrument Menu 150
- Windows Menu 151
- Help Menu 152
- System Control Toolbar 153
- 2000 MS Method Basic Scan 155
- Functions 155
- 2000 MS Method Chemical 157
- Ionization 157
- The CI Parameters 160
- Ejection Amplitude (v) 161
- Background mass 161
- Target TIC Value 161
- Maximum ionization time 161
- Maximum reaction time 161
- Prescan Ionization Time 162
- Using Liquid CI Reagents 164
- Choice of Liquid CI Reagents 165
- Than Methane 167
- Tuning for CI Operation 168
- Recommended Reading 169
- 2000 MS Method Command 171
- Reference 171
- The flow sampling segment 172
- Ionization Mode 173
- Ion Preparation 173
- Segment Setpoints 174
- Ionization Mode - EI Auto 175
- Ionization Mode - EI Fixed 176
- CI Fixed Parameters 178
- Ion Storage (SIS) Parameters 179
- Customize SIS 179
- The MS/MS Ion Prep Method 180
- Item Description 181
- Customize Resonant Method 182
- Ion Preparation MS/MS 185
- 2000 MS Method Electron 191
- Ion Formation 192
- AGC Prescan 192
- Mass Scanning 193
- Software Parameters 195
- Mass Range Segment Breaks 197
- Ionization Storage Level 197
- Ionization Time Factor 197
- Maximum Ionization Time 198
- Background Mass 198
- The Ion Preparation Method 201
- Autoscale Waveform 206
- Tips for Using SIS 207
- Theory of Operation 209
- Parent Ion Isolation 210
- Product Ion Formation 210
- Product Ion Mass Scanning 213
- Chemical Ionization 213
- Control 213
- Summary 213
- The MS “q” Calculator 216
- Isolation 217
- Dissociation 220
- Excitation amplitude (volts) 224
- Parent ion 224
- Product ion 1 224
- Product ion 2 224
- Using Nonresonant Excitation 225
- MS/MS/MS 226
- 2000 MS Method Section 229
- The Method Builder Window 232
- The 2000 MS Method Windows 233
- The Flow Sampling Segment 235
- The Startup Method 237
- Status Window 238
- Importing Method Sections 239
- Deleting Method Sections 240
- Printing the Method 241
- Password Protecting a Method 241
- 3800 GC Method Command 243
- Default Clean Section 244
- Clean Mode Section 245
- Internal Standard Section 246
- Solvent Plug Settings 247
- User Defined Settings 248
- Viscosity Settings 248
- 3800 GC Sample Delivery 250
- 3800 GC Injector 251
- 1061 Injector 252
- 1079 Injector 252
- Spilt Ratio Dialog Box 253
- 3800 GC Flow/Pressure 255
- Type 4 (for valved systems) 257
- 3800 GC Column Oven 258
- 3800 GC Detector 259
- FID Detector 260
- TCD Detector 261
- TSD Detector 262
- ECD Detector 264
- PFPD Detector 265
- Methanizer Dialog Box 266
- 3800 GC Output 267
- 3800 GC Data Acquisition 268
- 3800 GC Method Section 269
- MS Workstation 270
- The 3800 GC Method Windows 273
- Spreadsheet editing 274
- Checking Method End times 275
- Sample Delivery Window 276
- Injector Window 278
- 1177 Injector 280
- 1041 Injector 281
- SPT Injection Device 282
- Flow/Pressure Window 283
- Pressure spreadsheet 286
- Flow spreadsheet 286
- Column Oven Window 287
- Detector Window 288
- Micro-TCD Detector 292
- Output Window 296
- Data Acquisition Window 297
- Autosampler Window 298
- Hardware 299
- 3800 GC System Control 305
- Command Reference 305
- 3800 Operation Display 306
- Temp Zones Status Display 307
- Component Status Display 307
- Column Oven Status: 308
- AutoSampler Status: 309
- Sample Delivery Status: 310
- Name Default State Energized 310
- 1041/1061 Injector Status: 312
- SPT Injector Status: 313
- FID Status: 317
- ECD Status: 319
- TSD Status: 319
- PFPD Status: 320
- 8400/8410 Carrousel Display 324
- Chromatogram Display Toolbar 325
- 3800 Setup Dialog Box 326
- Field Description 328
- 3900 GC Method Command 335
- 3900 GC Injector Section 343
- Type 1 (for 1177 injector) 345
- 3900 GC Column Oven Section 346
- 3900 GC Method Section 347
- The 3900 GC Method Windows 351
- GC Control Window 354
- Injector Section 355
- Column Oven Section 357
- 3900 GC System Control 365
- Oven Status Display 367
- Injector EFC Status Display 368
- 3900 Setup Dialog Box 369
- 8200 AutoSampler Instrument 383
- Control Command Reference 383
- Hardware Dialog Box 386
- Automix Routines Dialog Box 387
- Carrousel Dialog Box 389
- 8200 Configuration Window 391
- Liquid Sampling Options 392
- User Defined Parameters 393
- SPME Options 394
- Main Toolbar 399
- Print Setup Dialog Box 402
- Edit Notes Dialog Box 403
- RecalcList Window 404
- Open Data File Dialog Box 409
- SampleList Window 410
- Sequence Window 416
- Automation File Editor 417
- GC Batch Report 427
- Method Selection 428
- Generating Reports 429
- Changing Report Commands 429
- GC Data Handling Calibration 431
- Automated Calibration 432
- Select View Curves 435
- Calibration Verification 436
- Introduction 437
- Performing a Pilot Run 437
- Peak Detection 438
- Rejecting Solvent Peaks 439
- Skimming Fused Peaks 439
- Splitting Fused Peaks 440
- Forcing Peaks 440
- Identifying Peaks 441
- Building a Calibration Curve 441
- Choosing a Calibration Type 443
- GC Data Handling Method 445
- Peak Table 447
- Calibration Setup 449
- Coefficients Table 451
- Calibration Curve Window 452
- This Report Only Dialog Box 453
- Print All Dialog Box 454
- Overlay Window 454
- Point Info Dialog Box 455
- Coefficients Dialog Box 455
- Verification Setup 456
- Time Events Table 457
- Time Events 458
- Event Description 459
- Run Information 463
- Open Method File Dialog Box 464
- Save Method As Dialog Box 466
- Preferences Dialog Box 467
- Layout Tab 468
- Trace Settings Tab 469
- Offsets Tab 471
- Colors Tab 472
- Fill Peak Table Window 475
- Exact View Dialog Box 476
- File Menu 477
- View Menu 478
- Results Menu 479
- Edit Method Menu 480
- Toolbar Overview 483
- Method Quick Link Toolbar 484
- Chromatogram Toolbar 484
- Locator Window 487
- Main Window 488
- Opening Data Files 489
- Zooming and Scrolling 489
- Autoscaling 490
- Moving Baselines 490
- Info-Panels 491
- Cursor Info-Panel 492
- Run File Info-Panel 492
- Visual Method Edit Window 493
- Types of Time Events 494
- Right Mouse Menus 496
- Action Effect of Action 497
- GC Interactive Graphics 499
- The Locator Window 500
- Changing Viewing Options 503
- The Preferences Dialog Box 504
- Offsets 505
- Selecting a Method 506
- Integration Parameters 509
- Filling the Peak Table 512
- These events are selected 514
- Calculating Results 515
- Viewing Results 517
- Viewing Calibration Curves 518
- GC Standard Report Method 521
- Results Format 523
- Chromatogram Format 524
- Print Options 527
- Automated Report Generation 530
- Select Printer Setup 531
- Specify a Print action 532
- Select the Data File 534
- Method Builder Dialog Boxes 537
- Add Password Dialog Box 540
- Change Password Dialog Box 541
- Star Assistant Wizard 545
- Select Configuration 546
- Configure Modules 547
- Confirm Configuration 550
- Method Builder Menus 551
- Window Menu 552
- Method Builder Toolbars 555
- Directory Toolbar 556
- Window Toolbar 557
- Method Builder Window 559
- Method Directory 560
- Method Parameters 561
- Module Information Editor 563
- Creating a Section 564
- Deleting a Section 564
- Renaming a Section 564
- Adding an Entry to a Section 565
- Commands 567
- Dialog Boxes 568
- Security Administration 571
- Application Locking 573
- File Revision Settings 574
- Standard GC Reports Command 577
- Options Menu 578
- Print Dialog Box 582
- Printer Setup Dialog Box 583
- Title Dialog Box 583
- Results Options Dialog Box 586
- Find Dialog Box 587
- Standard GC Reports Format 589
- Descriptions 589
- Verification Report 595
- Standard GC Reports Toolbar 597
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