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Chapter
3 Peak Detecti
on and Labe
ling
3-
74
Applied Biosystems
3
1
2
...
167
168
169
170
171
172
173
174
175
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...
446
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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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