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Using the Peptide Fragmentation Toolbox
Data Explorer
™
Software User’s Guide C-11
C
• y and b pairsLists peak pairs whose
combined masses plus 1 Da add up to the
Precursor Ion Mass you specified on the
Setup tab.
• Loss of H2O Lists peak pairs with a 18 Da
mass difference.
3. To remove all pairs results, click Clear List.
4. To remove a mass from the Spec Peak List (to simplify the
sequence interpretation), select an entry in the pairs
results, then click Left or Right under Remove Mass.
5. Click Copy to Output Window Result Tab to copy
results to the Result tab. You can then copy from the
Result tab to another application such as Notepad, or
print, as needed.
Sequence To list ion sequences:
1. Click the Sequence tab.
Figure 3-12 Peptide FragmentationSequence
- Data Explorer 1
- Software 1
- Data Explorer 5
- Software User’s Guide v 5
- Software User’s Guide vii 7
- Chapter 9 Troubleshooting 8
- (Visual Basic Macros) 9
- Table of Contents 10
- How to Use This Guide 11
- Notes, Cautions 13
- Warnings, and 13
- Send us your 14
- 1 Data Explorer 15
- 1.1 Overview 16
- Starting and 17
- 1-4 Applied Biosystems 18
- 1.2 File Formats and Types 19
- 1-6 Applied Biosystems 20
- File Formats and Types 21
- Software User’s Guide 1-7 21
- Additional files 22
- Software User’s Guide 1-9 23
- 1-10 Applied Biosystems 24
- 1.3 Parts of the 25
- Data Explorer Window 25
- Software User’s Guide 1-13 27
- Context-sensitive 28
- Output window 29
- 1.4 Customizing the 31
- 1-18 Applied Biosystems 32
- Software User’s Guide 1-19 33
- Opening 34
- Applying a .SET 34
- 1.4.3 Customizing Toolbars 35
- Undocking 36
- 1.5 Setting Graphic Options 37
- Accessing 38
- Setting Graphic Options 39
- Software User’s Guide 1-25 39
- Setting line 40
- Setting data 41
- Setting traces in 42
- Line or Vertical 42
- Bar mode 42
- Setting graphic 42
- Software User’s Guide 1-29 43
- 1.6 Managing Files 44
- Managing Files 45
- Software User’s Guide 1-31 45
- Viewing file 46
- Searching file 46
- 1.6.2 Converting Data from 47
- 1.6.3 Converting to and 48
- Exporting ASCII Data 48
- Importing a Trace 49
- Exporting .BIC 50
- .MSM, and .CAL 50
- Software User’s Guide 1-37 51
- Saving .LBS 52
- Copy displayed 53
- 1-40 Applied Biosystems 54
- Software User’s Guide 1-41 55
- 1-42 Applied Biosystems 56
- 2 Using Chromatogram 57
- 2.1.1 Opening Data Files 58
- 2-4 Applied Biosystems 60
- Software User’s Guide 2-5 61
- Software User’s Guide 2-7 63
- Using Activate 64
- Software User’s Guide 2-9 65
- 2.1.6 Closing Data Files 66
- Adjusting the Display Range 67
- Software User’s Guide 2-11 67
- 2-12 Applied Biosystems 68
- 2.3 Organizing Windows 69
- 2.4 Manipulating Traces 70
- 2.4.2 Duplicating a Trace 71
- 2.4.4 Adding Traces from 72
- Setting the 73
- Replace mode 73
- 2-18 Applied Biosystems 74
- Manipulating Traces 75
- Software User’s Guide 2-19 75
- 2-20 Applied Biosystems 76
- 2.4.5 Removing Traces 77
- (Processing History) 78
- History options 79
- 2.4.8 Overlaying Traces 80
- Overlaying traces 81
- 2-26 Applied Biosystems 82
- Software User’s Guide 2-27 83
- 2.4.9 Annotating Traces 84
- Annotating the 85
- 2.4.10 Viewing Trace Labels 86
- Spectrum trace 87
- 2-32 Applied Biosystems 88
- 2.4.11 Printing Traces 89
- 2-34 Applied Biosystems 90
- Dedicating a 91
- 2-36 Applied Biosystems 92
- 2.5.2 Copying Traces from 93
- 2.6 Saving, Opening, and 94
- Deleting .DAT Results 94
- 2.7 Exporting, Opening, and 95
- Files (Mariner Data Only) 95
- .SPC Results Files 96
- Deleting results 97
- 2-42 Applied Biosystems 98
- 3 Peak Detection 99
- 3.1 Overview 100
- 3.1.2 The Resolution-Based 101
- Peak Detection Routine 101
- 3-4 Applied Biosystems 102
- Voyager data 103
- Overlapping peak 103
- PSD peak 103
- 3.2 Peak Detection 104
- Peak Detection 105
- Software User’s Guide 3-7 105
- 3-8 Applied Biosystems 106
- Software User’s Guide 3-9 107
- 3-10 Applied Biosystems 108
- Software User’s Guide 3-11 109
- 3-12 Applied Biosystems 110
- Setting Basic 111
- Settings 111
- (spectrum data) 111
- 3-14 Applied Biosystems 112
- Software User’s Guide 3-15 113
- Setting Peak 114
- Processing 114
- (spectrum data 114
- Setting Advanced 115
- Resetting Basic 116
- 3.2.4 Peak Detection 117
- Parameter Descriptions 117
- Continued 118
- Software User’s Guide 3-21 119
- Software User’s Guide 3-25 123
- Software User’s Guide 3-27 125
- Software User’s Guide 3-31 129
- 3.2.5 Charge State 130
- Determination and Examples 130
- Max Charge State 131
- 3-34 Applied Biosystems 132
- Max Isotope # 133
- Effect of Minimum 134
- Intensity 134
- Charge state 134
- 3.3 Peak List 135
- Contents 136
- Chromatogram 136
- Procedure To insert peaks: 137
- 3.3.3 Saving the Peak List 138
- Importing and 139
- 3.3.4 Sorting, Filtering 140
- Peak List 141
- Software User’s Guide 3-43 141
- Printing 142
- Deleting items 142
- 3.4 Deisotoping a Spectrum 143
- 3-46 Applied Biosystems 144
- Deisotoping a Spectrum 145
- Software User’s Guide 3-47 145
- Using the 146
- Deisotope 146
- Software User’s Guide 3-49 147
- 3-50 Applied Biosystems 148
- Returning to the 149
- 3.5 Peak Labeling 150
- 3.5.1 Charge State Labels 151
- 3.5.2 Setting Chromatogram 152
- Peak Labeling 153
- Software User’s Guide 3-55 153
- 3-56 Applied Biosystems 154
- Software User’s Guide 3-57 155
- 3-58 Applied Biosystems 156
- Labels not 157
- Charge state 158
- Software User’s Guide 3-61 159
- 3-62 Applied Biosystems 160
- Software User’s Guide 3-63 161
- 3-64 Applied Biosystems 162
- Applying user 163
- Displaying user 163
- User labels not 164
- 3.6 Process that Occurs 165
- During Peak Detection 165
- Centroiding, and Integration 165
- 3-68 Applied Biosystems 166
- After peak 167
- 3-70 Applied Biosystems 168
- Default .SET files 169
- 3-72 Applied Biosystems 170
- Additional 171
- Voyager .SET files 171
- 3-74 Applied Biosystems 172
- Chromatogram Data 173
- 4 Examining 173
- 4.1 Overview 174
- Types of 175
- 4-4 Applied Biosystems 176
- 4.2 Creating an 177
- Extracted Ion Chromatogram 177
- 4-6 Applied Biosystems 178
- Software User’s Guide 4-7 179
- From the 180
- Spectrum window 180
- 4.2.2 Creating a Constant 181
- 4-10 Applied Biosystems 182
- Software User’s Guide 4-11 183
- 4-12 Applied Biosystems 184
- 4.3 Creating an Extracted 185
- Absorbance Chromatogram 185
- (XAC) (Mariner Data Only) 185
- 4-14 Applied Biosystems 186
- 4-16 Applied Biosystems 188
- Noise Filtering/Smoothing 189
- Software User’s Guide 4-17 189
- 4-18 Applied Biosystems 190
- Software User’s Guide 4-19 191
- 4.5 Adding and Subtracting 192
- Software User’s Guide 4-21 193
- 4-22 Applied Biosystems 194
- (Mariner Data Only) 195
- Filtering 196
- Software User’s Guide 4-25 197
- Evaluating 198
- Displaying 198
- 4.7 Adjusting the Baseline 199
- 4-28 Applied Biosystems 200
- Adjusting the Baseline 201
- Software User’s Guide 4-29 201
- 4.8 Using UV Trace Offset 202
- Software User’s Guide 4-31 203
- 4-32 Applied Biosystems 204
- 5 Examining 205
- Spectrum Data 205
- 5.1 Overview 206
- 5-4 Applied Biosystems 208
- 5.3 Manual Calibration 209
- 5-6 Applied Biosystems 210
- 5.3.2 Manually Calibrating 211
- Manually 212
- Manual Calibration 213
- Software User’s Guide 5-9 213
- Manually matching 214
- Software User’s Guide 5-11 215
- Eliminating data 216
- Software User’s Guide 5-13 217
- Automatically 218
- Applying new 219
- 5-16 Applied Biosystems 220
- Software User’s Guide 5-17 221
- 5-18 Applied Biosystems 222
- Software User’s Guide 5-19 223
- Modifying a 224
- Specifying mass 225
- 5-22 Applied Biosystems 226
- Software User’s Guide 5-23 227
- Ensuring that 228
- Importing a 229
- 5.4 Automatic Calibration 230
- Automatic 231
- Mariner data 231
- Importing 233
- 5-30 Applied Biosystems 234
- Automatic Calibration 235
- Software User’s Guide 5-31 235
- 5-32 Applied Biosystems 236
- Saving the .SET 237
- Software User’s Guide 5-35 239
- 5.5 Centroiding 240
- 5.6 Mass Deconvolution 241
- 5-38 Applied Biosystems 242
- Software User’s Guide 5-39 243
- Converting to 244
- Software User’s Guide 5-41 245
- 5-42 Applied Biosystems 246
- Software User’s Guide 5-43 247
- 5-44 Applied Biosystems 248
- 5.8 Adjusting the Baseline 249
- 5-46 Applied Biosystems 250
- Software User’s Guide 5-47 251
- 5-48 Applied Biosystems 252
- Correcting the 253
- (continued) 254
- Software User’s Guide 5-53 257
- 5-54 Applied Biosystems 258
- 5.9 Truncating a Spectrum 260
- Truncating a Spectrum 261
- Software User’s Guide 5-57 261
- 5-58 Applied Biosystems 262
- Spectrum (Mariner Data Only) 263
- 5-60 Applied Biosystems 264
- Software User’s Guide 5-61 265
- Effect on Mariner 267
- .RST files 267
- Processed Spectra from the 268
- Same or Different Data Files 268
- Software User’s Guide 5-65 269
- 5-66 Applied Biosystems 270
- 6 Using Tools and 271
- Applications 271
- 6.1 Using the Elemental 272
- Composition Calculator 272
- Software User’s Guide 6-3 273
- 6-4 Applied Biosystems 274
- Electron state for 275
- If no results are 276
- 6.1.2 Setting Limits 277
- 6-8 Applied Biosystems 278
- Adding new 279
- Figure 6-6 Periodic Table 280
- Software User’s Guide 6-11 281
- Setting limits for 282
- Using the Isotope 283
- Calculator 283
- 6-14 Applied Biosystems 284
- Using the Isotope Calculator 285
- Software User’s Guide 6-15 285
- Add and subtract 286
- Software User’s Guide 6-17 287
- If results are not 289
- 6.3 Using the 290
- Mass Resolution Calculator 290
- Software User’s Guide 6-21 291
- 6-22 Applied Biosystems 292
- 6-24 Applied Biosystems 294
- 6.5 Using the 295
- Ion Fragmentation Calculator 295
- 6-26 Applied Biosystems 296
- Software User’s Guide 6-27 297
- Calculating the 298
- Software User’s Guide 6-29 299
- Creating a 300
- 6.6 Using the Elemental 301
- Targeting Application 301
- 6-32 Applied Biosystems 302
- Displaying the 303
- 6.7 Using the Macro Recorder 304
- 6-36 Applied Biosystems 306
- 6.7.2 Recording a Macro 307
- Assigning a 308
- 6.7.4 Running a Macro 309
- If the macro 310
- 6.7.5 Deleting a Macro 311
- 6.7.6 Advanced Macro Editing 312
- Importing when 313
- Exporting To export macros: 314
- Using the Macro Recorder 315
- Software User’s Guide 6-45 315
- 6-46 Applied Biosystems 316
- 7 Data Explorer 317
- Examples 317
- 7.1 Mariner Data Examples 318
- Mariner Data Examples 319
- Software User’s Guide 7-3 319
- 7.1.2 Deconvoluting and 320
- Evaluating Unresolved 320
- Chromatographic Peaks 320
- Creating 321
- Software User’s Guide 7-7 323
- 7.1.3 Determining if a Peak 324
- Software User’s Guide 7-9 325
- 7.2 Voyager Data Examples 327
- Adjusting peak 328
- Voyager Data Examples 329
- Software User’s Guide 7-13 329
- Optimize Mass Accuracy 330
- Software User’s Guide 7-15 331
- 7-16 Applied Biosystems 332
- Software User’s Guide 7-17 333
- 7.2.3 Detecting Peaks 334
- Setting detection 335
- Basic Settings Tab 336
- Software User’s Guide 7-21 337
- Increasing 338
- 8 Viewing 339
- Voyager PSD Data 339
- 8.1 Displaying PSD Data 340
- Displaying PSD Data 341
- Software User’s Guide 8-3 341
- 8-4 Applied Biosystems 342
- Redisplaying the 343
- 8-6 Applied Biosystems 344
- Region of 345
- 8.2 Applying Fragment Labels 346
- Applying Fragment Labels 347
- Software User’s Guide 8-9 347
- When to use this 348
- Overview of 348
- .CAL file 348
- Calibrating a PSD Spectrum 349
- Software User’s Guide 8-11 349
- 8.3.2 Calibrating 350
- Software User’s Guide 8-13 351
- 8-14 Applied Biosystems 352
- Matching peaks 353
- Selecting peaks 354
- Software User’s Guide 8-17 355
- Solving and 356
- Selecting 357
- Creating PSD 358
- .CAL files 358
- 8.3.4 Creating PSD 359
- 8-22 Applied Biosystems 360
- When to change 361
- 8-24 Applied Biosystems 362
- 9 Troubleshooting 363
- 9.1 Overview 364
- 9.2 General Troubleshooting 365
- Chapter 9 Troubleshooting 366
- 9-4 Applied Biosystems 366
- General Troubleshooting 367
- Software User’s Guide 9-5 367
- 9.3 Processing, Tools, and 368
- Applications Troubleshooting 368
- Software User’s Guide 9-7 369
- 9-8 Applied Biosystems 370
- Software User’s Guide 9-9 371
- 9-10 Applied Biosystems 372
- Calibration Troubleshooting 373
- Software User’s Guide 9-11 373
- 9-12 Applied Biosystems 374
- Software User’s Guide 9-13 375
- 9.5 Printing Troubleshooting 376
- 9.6 Peak Detection and 377
- Labeling Troubleshooting 377
- 9-16 Applied Biosystems 378
- Software User’s Guide 9-17 379
- 9-18 Applied Biosystems 380
- Software User’s Guide 9-19 381
- 9-20 Applied Biosystems 382
- Software User’s Guide 9-21 383
- 9-22 Applied Biosystems 384
- Appendix 385
- Warranty period 386
- Warranty 386
- Warranties 387
- Appendix A Warranty 388
- A-4 Applied Biosystems 388
- B.1 Isotopes 390
- Isotopic pattern 391
- Isotope-limited 392
- Isotopes 393
- Software User’s Guide B-5 393
- B.2 Monoisotopic 394
- Figure B-7 Average Mass 395
- Average mass 395
- B-8 Applied Biosystems 396
- C.1 Overview 398
- C.2 Preparing Data 399
- Before Accessing Macros 399
- C.3 Accessing the Macros 400
- C.4 Using the 401
- Ladder Sequencing Toolbox 401
- C-6 Applied Biosystems 402
- Software User’s Guide C-7 403
- C.5 Using the Peptide 405
- Fragmentation Toolbox 405
- Pairs To list ion pairs: 406
- Software User’s Guide C-11 407
- C-12 Applied Biosystems 408
- Software User’s Guide C-13 409
- C.6 Using the 411
- Polymer Analysis Toolbox 411
- C-16 Applied Biosystems 412
- Calculations 413
- Preparing data 414
- MS Fit/MS tag 414
- Using MS Fit/MS Tag Toolbox 415
- Software User’s Guide C-19 415
- C-20 Applied Biosystems 416
- Numerics and Symbols 417
- Index-2 Applied Biosystems 418
- Index-4 Applied Biosystems 420
- Index-6 Applied Biosystems 422
- Index-8 Applied Biosystems 424
- Index-10 Applied Biosystems 426
- Index-12 Applied Biosystems 428
- Index-14 Applied Biosystems 430
- Index-16 Applied Biosystems 432
- Index-18 Applied Biosystems 434
- Index-20 Applied Biosystems 436
- Index-22 Applied Biosystems 438
- Index-24 Applied Biosystems 440
- Index-26 Applied Biosystems 442
- Index-28 Applied Biosystems 444
- Index-30 Applied Biosystems 446
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