Data Explorer™ Software
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How to Use This Guide
Chapter 1 Data Explorer™ Basics
Chapter 2 Using Chromatogram and Spectrum Windows
Chapter 3 Peak Detection and Labeling
Chapter 4 Examining Chromatogram Data
Chapter 5 Examining Spectrum Data
Chapter 6 Using Tools and Applications
Chapter 7 Data Explorer Examples
Chapter 8 Viewing Voyager PSD Data
Chapter 9 Troubleshooting
Appendix C Data Explorer Toolbox
Index
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How to Use This Guide
Purpose of this guide
Audience
Structure of this guide
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Conventions
Notes, Cautions
Warnings, and
Hints
Related documentation
Send us your comments
Chapter
1Data Explorer™ Basics
This chapter contains the following sections:
11.1 Overview
Features
Starting and exiting the software
Default colors
1.2.1Software Applications Compatibility
1.2.2 Data (.DAT) File Format
Mariner .SPC file
1 format
Voyager .MS file format
Extracting information from
.DAT files
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Additional files
types
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1.3 Parts of the
Data Explorer Window
Toolbar
and Spectrum
windows
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Tabs for data files
Data file names
Output window
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1.5.1 Changing Background Color
1 1.5.2 Customizing Graphic Options
Setting colors
Setting line widths
Setting data cursors
Setting traces in 1 Line or Vertical Bar mode
Setting graphic compression
1.5.3 Reverting to Previous Graphic Options
1.6.1Converting .SPC File Format to .DAT File Format (Mariner Data Only)
Converting
Viewing file properties
Searching file properties
1.6.2 Converting Data from
Profile to Centroid (Mariner Data Only)
1 1.6.3 Converting to and Exporting ASCII Data
1.6.4 Importing a Trace in ASCII Format
1.6.5Extracting and Saving Information from .DAT, .RSD, and .RCD Files
Saving .SET files
1.6.6 Copying from Data Files
Copy trace data
Copy displayed peaks
Copy all peaks
Copy mass list
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2Using Chromatogram and Spectrum Windows
Opening Data Files
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2.1.2 Displaying Mariner DAD Traces
Displaying Voyager Chromatograms
Viewing Read-OnlyFiles
2.1.5 Moving Between Open Files
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Closing Data Files
2.2 Adjusting the Display Range
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2.3 Organizing Windows
Linking views
Organizing windows
2.4.1Zooming, Centering, and Customizing a Trace
2.4.2 Duplicating a Trace
2.4.3Dividing the Active Trace
2.4.4Adding Traces from
the Same Data File to a Window
Setting the Replace mode
Adding a trace
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2.4.5 Removing Traces
2.4.6 Expanding and Linking Traces
2.4.7Recalling and Rearranging Traces (Processing History)
Setting Processing History options
2.4.8 Overlaying Traces
Overlaying traces in a single data file
Changing the active trace
Sequentially activating overlaid spectra
Setting overlay attributes
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2.4.9 Annotating Traces
Annotating the trace
2.4.10 Viewing Trace Labels
Spectrum trace
labels
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2.4.11 Printing Traces
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Dedicating a printer to landscape orientation
Print Setup
2.5.1 Working with Separate Data Files
2.5.2 Copying Traces from
Multiple Data Files to a Window
Comparing copied traces
2.6 Saving, Opening, and
Deleting .DAT Results
Saving results for
Opening results for .DAT files
Deleting results for .DAT files
Exporting results for .RCD and
.RSD files
Opening results for .RCD and
Deleting results for .RCD and .RSD files
Saving, Opening, and Deleting
.SPC Results Files
(Mariner Data Only)
.SPC files
Opening results: for .SPC files
Deleting results for .SPC files
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3Peak Detection and Labeling
3.1.1Default Peak Detection
3.1.2The Resolution-BasedPeak Detection Routine
Detection ranges
PSD peak detection for Voyager data
3.2.1Strategy for Mariner Peak Detection
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3.2.2 Strategy for Voyager Peak Detection
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3.2.3 Setting Peak Detection Parameters
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Setting Basic Settings (spectrum data)
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Setting Peak Processing parameters (spectrum data only)
Setting Advanced Settings (spectrum data only)
Resetting Basic
Settings
3.2.4Peak Detection Parameter Descriptions
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Basic Settings (spectrum data only)
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Peak Processing parameters (spectrum data only)
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Advanced
Settings (spectrum data only)
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3.2.5Charge State
Determination and Examples
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Charge state determination troubleshooting
3.3.1Displaying the Peak List
Contents of peak list
3.3.2 Inserting Peaks in the Peak List
3.3.3 Saving the Peak List
Importing and saving in Excel
3.3.4Sorting, Filtering
and Printing the Peak List
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Printing the peak list
Deleting items from the peak list
3.4 Deisotoping a Spectrum
During peak deisotoping
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Requirements
Deisotope
function
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3.5 Peak Labeling
Factors affecting peak labeling
Labeling peaks manually
3.5.1 Charge State Labels
3.5.2Setting Chromatogram and Spectrum Peak Labels
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Setting spectrum labels
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Deleting labels
Labels not displayed
Charge state not displayed
3.5.3 Setting Custom Peak Labels
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Applying user labels from .LBC or .LBS files
Displaying user labels
User labels not displayed
3.6Process that Occurs During Peak Detection, Centroiding, and Integration
Peak detection
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Centroiding
Integration
3.7 Default Peak Detection Settings
Default .SET files provided
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Additional Voyager .SET files provided
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4Examining Chromatogram Data
4.1 Overview
Types of Mariner data
Types of Voyager data
Creating macros to combine processing functions
Returning to the original trace
4.2.1Creating an Extracted
Ion Chromatogram (XIC)
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4.2.2Creating a Constant
Neutral Loss (CNL) Chromatogram
Labeling spectrum peaks with mass difference (optional)
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4.3Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)
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4.4 Noise Filtering/Smoothing
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4.5Adding and Subtracting
Raw Spectra Within a Data File
Adding and subtracting spectra
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4.6Displaying MS Method Data (Mariner Data Only)
In this section
Example applications
Displaying acquisition conditions and event tags
Setting Trace Replace mode
Filtering event tags
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Evaluating filtered traces
Displaying additional filtered traces
4.7.1Using Baseline Offset
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4.7.2 Using Baseline Correction
4.8Using UV Trace Offset (Mariner Data Only)
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5Examining Spectrum Data
5.1 Overview
Types of spectra you can display
Voyager PSD spectra
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5.2 Creating a Combined Spectrum
5.3.1 Overview of Manual Calibration
Calibration references files (.REF) provided
When to use manual calibration
Accurate mass
5 measurements
5.3.2 Manually Calibrating
Manually calibrating a single spectrum
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Exporting calibration constants (.CAL file)
Applying new constants to additional files
5.3.3Creating or Modifying a Calibration Reference File (.REF)
Definition
.REF files provided
Calibration reference file contents
Creating and saving a calibration reference file
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Modifying a calibration reference file
Specifying mass type for highly charged, narrow peaks
5.3.4 Reverting to Instrument Calibration
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5.3.5 Hints for Calibrating Mariner Data
5.3.6 Hints for Calibrating Voyager Data
5.4.1 Overview of Automatic Calibration
Automatic calibration for Mariner data
Automatic calibration for Voyager data
5.4.2Importing and Specifying Automatic Calibration Settings
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Saving the .SET file
5.4.3Automatically Calibrating (Mariner Data Only)
Calibration results
Applying auto calibration settings to other files
5.5 Centroiding
5.6Mass Deconvolution (Mariner Data Only)
Mass Deconvolution
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Converting to zero-charge
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5.7 Noise Filtering/Smoothing
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5.8.1Using Baseline Offset
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5.8.2 Using Baseline Correction
5.8.3 Using Advanced Baseline Correction
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General guidelines for setting parameters
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5.9 Truncating a Spectrum
Truncating
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5.10Converting to a Singly Charged Spectrum (Mariner Data Only)
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5.11AutoSaturation Correction (Mariner Data Only)
Function
Hardware
5 requirements
Effect on Mariner
.RST files
Trace label
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6Using Tools and Applications
6.1.1Determining Elemental Composition
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Calculating 14. Click Calculate
If no results are displayed
6.1.2 Setting Limits
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Adding new elements and setting limits
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Setting limits for
other result types
6.2 Using the Isotope Calculator
Using the Isotope
Calculator
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Add and subtract examples
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Evaluating traces
If results are not calculated
6.3 Using the
Mass Resolution Calculator
Calculating mass
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6.4 Using the Signal-to-NoiseRatio
Calculator
Calculating signal-to-noiseratio
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6.5 Using the
Ion Fragmentation Calculator
Using the Ion
Fragmentation
calculator
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Labeling peaks
Creating a calibration reference file (.REF)
6.6 Using the Elemental
Targeting Application
Elemental
application
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Displaying results
6.7.1Before Using the Macro Recorder
Location of macros
Displaying the macro toolbar
Functions not supported
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6.7.2 Recording a Macro
6.7.3 Assigning Macros to Buttons
6.7.4 Running a Macro
If the macro contains a syntax error
6.7.5 Deleting a Macro
6.7.6 Advanced Macro Editing
6.7.7 Importing or Exporting Macros
in DATAEXPLORER.VB6
Exporting
6.7.8 Running Macros Automatically
When Opening and Closing Files
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7Data Explorer Examples
Improving Signal-To-NoiseRatio
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7.1.2Deconvoluting and Evaluating Unresolved Chromatographic Peaks
Creating extracted ion chromatograms
Creating combined spectra
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7.1.3Determining if a Peak is Background Noise
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Creating extracted ion chromatogram
7.2.1 Detecting and Labeling
Partially Resolved Peaks
Adjusting peak
detection
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7.2.2Processing Before Calibrating to Optimize Mass Accuracy
Before calibrating
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7.2.3Detecting Peaks
from Complex Digests
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8Viewing
Voyager PSD Data
8.1 Displaying PSD Data
Displaying the composite spectrum
Advancing through segment traces
Displaying multiple segment traces
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Redisplaying the composite spectrum
How the composite spectrum is generated
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8.2 Applying Fragment Labels
Applying labels
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8.3 Calibrating a PSD Spectrum
When to use this procedure
Overview of creating a PSD
.CAL file
8.3.1 Checking Peak Detection
8.3.2 Calibrating
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Matching peaks automatically
Selecting peaks manually
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Solving and plotting
Selecting calibration peaks for optimum mass accuracy
8.3.3Creating PSD Calibration (.CAL) Files and Applying to Other Data Files
8.3.4Creating PSD
Calibration Reference (.REF) Files
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8.3.5 Changing the Precursor Mass
Changing
9 Troubleshooting
9.1 Overview
9.2 General Troubleshooting
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9.3Processing, Tools, and Applications Troubleshooting
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9.4 Calibration Troubleshooting
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9.5 Printing Troubleshooting
9.6Peak Detection and Labeling Troubleshooting
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A Warranty
Warranty period effective date
Warranty claims
Warranty exceptions
Warranties limitations
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BOverview of Isotopes
B.1 Isotopes
Isotopic pattern in mass spectra
Isotope-limitedresolution
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B.2 Monoisotopic
and Average Masses
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B.3 Isotopes of Common Elements
This appendix includes:
C.1 Overview
Modifying the macros
References required
C.2 Preparing Data
Before Accessing Macros
C.3 Accessing the Macros
C.4 Using the
Ladder Sequencing Toolbox
Running the
macro
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Displaying the
original labels
C.5 Using the Peptide
Fragmentation Toolbox
Setup
Pairs
Sequence
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Correlation
Displaying the original labels
C.6 Using the
Polymer Analysis Toolbox
Using Polymer Analysis
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Calculations
C.7 Using MS Fit/MS Tag Toolbox
Preparing data before accessing
Running
MS Fit/MS tag
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Index
