Manuals
/
Brands
/
Computer Equipment
/
Calculator
/
HP
/
Computer Equipment
/
Calculator
HP
Data Explorer 4 manual
1
1
447
447
Download
447 pages, 3.68 Mb
Data Explorer
™
Software
Version 4 Series Software
User Guide
Contents
Data Explorer™ Software
Page
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
Page
How to Use This Guide
Purpose of this guide
Audience
Structure of this guide
Page
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
Page
Additional files
types
Page
Page
1.3 Parts of the
Data Explorer Window
Toolbar
and Spectrum
windows
Page
Tabs for data files
Data file names
Output window
Page
Page
Page
Page
Page
Page
Page
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
Page
2Using Chromatogram and Spectrum Windows
Opening Data Files
Page
Page
Page
2.1.2 Displaying Mariner DAD Traces
Displaying Voyager Chromatograms
Viewing Read-OnlyFiles
2.1.5 Moving Between Open Files
Page
Closing Data Files
2.2 Adjusting the Display Range
Page
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
Page
Page
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
Page
2.4.9 Annotating Traces
Annotating the trace
2.4.10 Viewing Trace Labels
Spectrum trace
labels
Page
2.4.11 Printing Traces
Page
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
Page
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
Page
3.2.2 Strategy for Voyager Peak Detection
Page
Page
3.2.3 Setting Peak Detection Parameters
Page
Setting Basic Settings (spectrum data)
Page
Page
Setting Peak Processing parameters (spectrum data only)
Setting Advanced Settings (spectrum data only)
Resetting Basic
Settings
3.2.4Peak Detection Parameter Descriptions
Page
Page
Basic Settings (spectrum data only)
Page
Page
Page
Peak Processing parameters (spectrum data only)
Page
Advanced
Settings (spectrum data only)
Page
Page
Page
3.2.5Charge State
Determination and Examples
Page
Page
Page
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
Page
Printing the peak list
Deleting items from the peak list
3.4 Deisotoping a Spectrum
During peak deisotoping
Page
Requirements
Deisotope
function
Page
Page
Page
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
Page
Setting spectrum labels
Page
Page
Deleting labels
Labels not displayed
Charge state not displayed
3.5.3 Setting Custom Peak Labels
Page
Page
Page
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
Page
Centroiding
Integration
3.7 Default Peak Detection Settings
Default .SET files provided
Page
Additional Voyager .SET files provided
Page
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)
Page
Page
Page
4.2.2Creating a Constant
Neutral Loss (CNL) Chromatogram
Labeling spectrum peaks with mass difference (optional)
Page
Page
4.3Creating an Extracted Absorbance Chromatogram (XAC) (Mariner Data Only)
Page
Page
Page
4.4 Noise Filtering/Smoothing
Page
Page
4.5Adding and Subtracting
Raw Spectra Within a Data File
Adding and subtracting spectra
Page
Page
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
Page
Evaluating filtered traces
Displaying additional filtered traces
4.7.1Using Baseline Offset
Page
4.7.2 Using Baseline Correction
4.8Using UV Trace Offset (Mariner Data Only)
Page
Page
5Examining Spectrum Data
5.1 Overview
Types of spectra you can display
Voyager PSD spectra
Page
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
Page
Page
Page
Page
Page
Page
Page
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
Page
Modifying a calibration reference file
Specifying mass type for highly charged, narrow peaks
5.3.4 Reverting to Instrument Calibration
Page
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
Page
Page
Page
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
Page
Page
Converting to zero-charge
Page
5.7 Noise Filtering/Smoothing
Page
Page
5.8.1Using Baseline Offset
Page
5.8.2 Using Baseline Correction
5.8.3 Using Advanced Baseline Correction
Page
Page
Page
Page
Page
General guidelines for setting parameters
Page
5.9 Truncating a Spectrum
Truncating
Page
Page
5.10Converting to a Singly Charged Spectrum (Mariner Data Only)
Page
Page
5.11AutoSaturation Correction (Mariner Data Only)
Function
Hardware
5 requirements
Effect on Mariner
.RST files
Trace label
Page
Page
Page
6Using Tools and Applications
6.1.1Determining Elemental Composition
Page
Page
Calculating 14. Click Calculate
If no results are displayed
6.1.2 Setting Limits
Page
Adding new elements and setting limits
Page
Page
Setting limits for
other result types
6.2 Using the Isotope Calculator
Using the Isotope
Calculator
Page
Page
Add and subtract examples
Page
Evaluating traces
If results are not calculated
6.3 Using the
Mass Resolution Calculator
Calculating mass
Page
Page
6.4 Using the Signal-to-NoiseRatio
Calculator
Calculating signal-to-noiseratio
Page
6.5 Using the
Ion Fragmentation Calculator
Using the Ion
Fragmentation
calculator
Page
Page
Page
Page
Labeling peaks
Creating a calibration reference file (.REF)
6.6 Using the Elemental
Targeting Application
Elemental
application
Page
Displaying results
6.7.1Before Using the Macro Recorder
Location of macros
Displaying the macro toolbar
Functions not supported
Page
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
Page
7Data Explorer Examples
Improving Signal-To-NoiseRatio
Page
7.1.2Deconvoluting and Evaluating Unresolved Chromatographic Peaks
Creating extracted ion chromatograms
Creating combined spectra
Page
7.1.3Determining if a Peak is Background Noise
Page
Creating extracted ion chromatogram
7.2.1 Detecting and Labeling
Partially Resolved Peaks
Adjusting peak
detection
Page
7.2.2Processing Before Calibrating to Optimize Mass Accuracy
Before calibrating
Page
Page
7.2.3Detecting Peaks
from Complex Digests
Page
Page
Page
Page
8Viewing
Voyager PSD Data
8.1 Displaying PSD Data
Displaying the composite spectrum
Advancing through segment traces
Displaying multiple segment traces
Page
Redisplaying the composite spectrum
How the composite spectrum is generated
Page
8.2 Applying Fragment Labels
Applying labels
Page
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
Page
Page
Matching peaks automatically
Selecting peaks manually
Page
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
Page
8.3.5 Changing the Precursor Mass
Changing
9 Troubleshooting
9.1 Overview
9.2 General Troubleshooting
Page
Page
9.3Processing, Tools, and Applications Troubleshooting
Page
Page
Page
9.4 Calibration Troubleshooting
Page
Page
Page
9.5 Printing Troubleshooting
9.6Peak Detection and Labeling Troubleshooting
Page
Page
Page
Page
Page
Page
Page
A Warranty
Warranty period effective date
Warranty claims
Warranty exceptions
Warranties limitations
Page
BOverview of Isotopes
B.1 Isotopes
Isotopic pattern in mass spectra
Isotope-limitedresolution
Page
B.2 Monoisotopic
and Average Masses
Page
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
Page
Page
Displaying the
original labels
C.5 Using the Peptide
Fragmentation Toolbox
Setup
Pairs
Sequence
Page
Correlation
Displaying the original labels
C.6 Using the
Polymer Analysis Toolbox
Using Polymer Analysis
Page
Calculations
C.7 Using MS Fit/MS Tag Toolbox
Preparing data before accessing
Running
MS Fit/MS tag
Page
Page
Index