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Data Explorer 4 Series
Applied Biosystems Data Explorer 4 Series Manuals
Manuals and User Guides for Applied Biosystems Data Explorer 4 Series. We have
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Applied Biosystems Data Explorer 4 Series manual available for free PDF download: User Manual
Applied Biosystems Data Explorer 4 Series User Manual (447 pages)
Data Explorer User Guide V4 Series SW User Guide
Brand:
Applied Biosystems
| Category:
Software
| Size: 3.85 MB
Table of Contents
Table of Contents
3
User Guide
1
How to Use this Guide
11
Chapter 1 ™ Basics
15
Overview
16
File Formats and Types
19
Software Applications Compatibility
19
Data (.DAT) File Format
19
Parts of the Data Explorer Window
25
Customizing the Data Explorer Window
31
Setting Default Values
31
Customizing Processing and Graphic Settings (.SET)
31
Customizing Toolbars
35
Setting Graphic Options
37
Changing Background Color
37
Customizing Graphic Options
38
Reverting to Previous Graphic Options
43
Converting .SPC File Format to .DAT File Format (Mariner Data Only)
44
Data Explorer™ Basics
44
Extracting and Saving Information
44
Converting Data from Profile to Centroid (Mariner Data Only)
47
Converting to and Exporting ASCII Data
48
Importing a Trace in ASCII Format
49
Extracting and Saving Information from .DAT, .RSD, and .RCD Files
50
Copying from Data Files
52
Managing Files
44
Chapter 2 And Spectrum Windows
57
Opening and Closing Data Files
58
Opening Data Files
58
Displaying Mariner DAD Traces
62
Displaying Voyager Chromatograms
63
Viewing Read-Only Files
63
Moving between Open Files
64
Closing Data Files
66
Adjusting the Display Range
67
Organizing Windows
69
Manipulating Traces
70
Zooming, Centering, and Customizing a Trace
70
Duplicating a Trace
71
Dividing the Active Trace
71
Adding Traces from the same Data File to a Window
72
Removing Traces
77
Expanding and Linking Traces
77
Recalling and Rearranging Traces (Processing History)
78
Overlaying Traces
80
Annotating Traces
84
Viewing Trace Labels
86
Printing Traces
89
Working with Multiple Data Files
92
Working with Separate Data Files
92
Copying Traces from Multiple Data Files to a Window
93
Saving, Opening, and Deleting .DAT Results
94
Exporting, Opening, and Deleting .RCD and .RSD Results Files (Mariner Data Only)
95
Saving, Opening, and Deleting .SPC Results Files (Mariner Data Only)
96
Chapter 3 And Labeling
99
Overview
100
Default Peak Detection
100
The Resolution-Based Peak Detection Routine
101
Peak Detection
104
Strategy for Mariner Peak Detection
104
Strategy for Voyager Peak Detection
106
Setting Peak Detection Parameters
109
Peak Detection Parameter Descriptions
117
Charge State Determination and Examples
130
Peak List
135
Displaying the Peak List
135
Inserting Peaks in the Peak List
137
Saving the Peak List
138
Deisotoping a Spectrum
143
Sorting, Filtering, and Printing the Peak List
144
Deisotoping a Spectrum
145
Peak Labeling
150
Charge State Labels
151
Setting Chromatogram and Spectrum Peak Labels
152
Setting Custom Peak Labels
159
Process that Occurs During Peak Detection, Centroiding, and Integration
165
Default Peak Detection Settings
169
Chapter 4 Chromatogram Data
173
Overview
174
Creating an Extracted Ion Chromatogram
177
Creating an Extracted Ion Chromatogram (XIC)
177
Creating a Constant Neutral Loss (CNL) Chromatogram
181
Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)
185
Noise Filtering/Smoothing
189
Adding and Subtracting Raw Spectra Within a Data File
192
Adding and Subtracting Spectra
192
Displaying MS Method Data
195
Displaying MS Method Data (Mariner Data Only)
195
Adjusting the Baseline
199
Using Baseline Offset
199
Using Baseline Correction
201
Using UV Trace Offset
202
Using UV Trace Offset (Mariner Data Only)
202
Chapter 5 Spectrum Data
205
Overview
206
Creating a Combined Spectrum
208
Manual Calibration
209
Overview of Manual Calibration
209
Manually Calibrating
211
Creating or Modifying a Calibration Reference File (.REF)
221
Reverting to Instrument Calibration
226
Hints for Calibrating Mariner Data
228
Hints for Calibrating Voyager Data
229
Automatic Calibration
230
Overview of Automatic Calibration
230
Importing and Specifying Automatic Calibration Settings
233
Automatically Calibrating (Mariner Data Only)
238
Centroiding
240
Mass Deconvolution (Mariner Data Only)
241
Noise Filtering/Smoothing
246
Adjusting the Baseline
249
Using Baseline Offset
249
Using Baseline Correction
251
Using Advanced Baseline Correction
252
Truncating a Spectrum
260
Converting to a Singly Charged Spectrum (Mariner Data Only)
263
Autosaturation Correction (Mariner Data Only)
266
Adding and Subtracting Raw or Processed Spectra from the same or Different Data Files (Dual Spectral Trace Arithmetic)
268
Chapter 6 Applications
271
Using the Elemental Composition Calculator
272
Determining Elemental Composition
272
Elemental Composition Calculator
273
Setting Limits
277
Using the Isotope Calculator
283
Using the Mass Resolution Calculator
283
Using the Mass Resolution Calculator
290
Using the Signal-To-Noise Ratio Calculator
290
Using the Signal-To-Noise Ratio Calculator
293
Using the Ion Fragmentation Calculator
295
Using the Elemental Targeting Application
301
Using the Macro Recorder
304
Before Using the Macro Recorder
304
Recording a Macro
307
Assigning Macros to Buttons
308
Running a Macro
309
Deleting a Macro
311
Advanced Macro Editing
312
Importing or Exporting Macros in DATAEXPLORER.VB6
313
Running Macros Automatically When Opening and Closing Files
315
Chapter 7 Examples
317
Mariner Data Examples
318
Improving Signal-To-Noise Ratio
318
Unresolved Chromatographic Peaks
320
Deconvoluting and Evaluating Unresolved Chromatographic Peaks
320
Unresolved Chromatographic Peaks
322
Determining if a Peak Is Background Noise
324
Voyager Data Examples
327
Detecting and Labeling Partially Resolved Peaks
327
Processing before Calibrating to Optimize Mass Accuracy
330
Detecting Peaks from Complex Digests
334
Chapter 8 Voyager Psd Data
339
Displaying PSD Data
340
Applying Fragment Labels
346
Calibrating a PSD Spectrum
348
Checking Peak Detection
349
Calibrating
350
Creating PSD Calibration (.CAL) Files and Applying to Other Data Files
358
Creating PSD Calibration Reference (.REF) Files
359
Changing the Precursor Mass
361
Table of Contents
363
Chapter 9 Troubleshooting
364
Overview
364
General Troubleshooting
365
Processing, Tools, and Applications Troubleshooting
368
Calibration Troubleshooting
372
Printing Troubleshooting
376
Peak Detection and Labeling Troubleshooting
377
Appendix A Warranty Information
390
Appendix B Overview of Isotopes
390
Appendix C Data Explorer Toolbox
390
Overview
390
Appendix C
397
Overview
398
C.1 Overview
398
This Appendix Includes:
398
Preparing Data before Accessing Macros
399
Before Accessing Macros
399
Accessing the Macros
400
Using the Ladder Sequencing Toolbox
401
Ladder Sequencing Toolbox
401
Using the Peptide Fragmentation Toolbox
405
Peptide Fragmentation Toolbox
405
Using the Polymer Analysis Toolbox
411
Using MS Fit/Ms Tag Toolbox
414
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