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Using the Peptide Fragmentation Toolbox
Data Explorer
™
Software User’s Guide C-9
C
C.5 Using the Peptide
Fragmentation Toolbox
Use the Peptide Fragmentation toolbox when examining
Voyager composite PSD spectra or Mariner in-source CID
spectra to label immonium ions, identify fragment ion pairs,
view sequences based on different reference peaks, and
determine if a selected peak is of a specific fragment ion
category.
Setup To enter Setup parameters for the Peptide Fragmentation
Toolbox macro:
1. In the Toolbox Palette dialog box, click Peptide
Fragmentation Toolbox.
Figure 3-10 Peptide FragmentationSetup
2. In the Setup tab, click Get Spec Peak List.
- 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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