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level of parent or product ions in the analytical scan results in consistent,
reproducible product ion spectra.
Lower target values may be required with the MS/MS option to prevent space
charging effects. Based on the isolated parent ion, the following target values are
recommended.
Parent Ion Target
60 m/z 150
10000
150 m/z 500
5000
500 m/z 650
2000
Additionally, the EI-Auto PreScan ionization time must be changed from the
default value. This is done automatically when the user selects MS/MS ion prep.
The PreScan ionization time is changed to 1500 µsec.
The MS/MS Ion Prep Method
MS/MS Software Parameters
Under the Isolation header, enter the Parent Ion Mass (m/z). The parent ion
mass range is 50 to 650 m/z.
NOTE: Integer mass values may be used if the mass isolation window (next
step) is greater than 1.5 m/z. If the window size is less than 1.5 m/z, or if the
mass defect of the parent ion is greater than approximately 0.3 m/z, use the
exact fractional mass.
- 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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