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Product Tree: Desktop Software > FreeStyle Software
Software version: 1.8 SP3

Preface
Open the FreeStyle application
Access Documentation
System Requirements
Special Notices
Contacting us
Introduction
Mass Spectra
Base peak
Neutral Losses
Effect of ionization modes
Ionization modes for LC/MS instruments
Ionization modes for GC/MS instruments
Adduct Formation
Effect of isotopes
Isotope patterns in High-Resolution data
Analysis Modes for the Mass Spectrometer
Full Scan
Selected Ion Monitoring (SIM)
MS/MS
Qualitative Analysis Tools
New Features and Enhancements
Use the FreeStyle window
Startup window
File Menu
Communicator Bar
Open raw data files or sequence files
Factory Default Layout
Hierarchy of the chromatogram and spectrum views
Use Workspace pages
Arrange views
Select the columns to display in a view or dialog box with tabular data
Save and apply Layout Templates
Restore the default settings
Use the pointer to update the timebase or rescale a graph
Pointer action and effects
Add text, graphic, and structure annotations to a Graphical view
Place a drawing object behind the plot
Draw a line
Draw a box or a filled box
Add a text label
Edit a text label
Remove one or more labels
Annotate a spectral peak with a structure
Save text and structure annotations in the Spectrum view
Import text and structure annotations
Copy, export, and print graphical images and tabular data
Copy an image of a graphical view to the clipboard
Copy tabular data to the clipboard
Export or print the contents of a view or workspace
Set the FreeStyle as the default data visualization application
Toolbars
Workspace Options toolbar
Display the Workspace Options toolbar
Workspace Processing toolbar
Display Options Toolbar
Zoom Options Toolbar
Text and Graphic Annotation Toolbar
Views
Info Bar Pages
Manage the Info Bar pages
Review Chromatographic Data
Add a Chromatogram view
Close a Chromatogram view
Effect of closing a Chromatogram view
Add Chromatogram traces
Supported chromatogram traces
Add Chromatogram traces manually
Add Chromatogram Traces with the auto filter feature
Display a filtered chromatogram
Specify the maximum number of chromatogram traces to display
Delete a Chromatogram trace
Define a Chromatogram Trace from the Chromatogram Ranges view
Manually defining Chromatogram Ranges
Manually specify the ranges of the chromatogram traces
Specify smoothing for a plot
Specify reference (fixed) plots
Define Chromatogram Ranges by using a spreadsheet file
Display Mass Defect Filtered Chromatogram traces
Mass Defect Filter parameters
Apply a Mass Defect Filter
Relative and absolute mass range calculation
Link a Spectrum view to an MDF chromatogram trace
Set up instrument status traces
Display an EIC Trace
Display an EIC trace for multiple discrete m/z values
Specify the mass ranges for an EIC trace
Use the Scan Filters page to display a filtered chromatogram
Set up the Display Options for a Chromatogram Trace
Format the Chromatogram plots
Label Chromatogram Peaks or Local Maxima
Add the peak area, peak height, and signal-to-noise labels to each detected peak
Fill the chromatogram peaks
Normalize Chromatogram Traces
Apply local normalization
Apply global normalization
Turn off Normalization
Change the Y-Axis range for normalized chromatograms
Change the Y-Axis title and scale of the Chromatogram view
Change the y-axis title of the Chromatogram view
Change the y-axis scale
Change the zoom level of a Chromatogram
Automatically detecting and integrating chromatographic peaks
Run any of the peak detection algorithms
Run the elemental composition algorithm
Check the integration for each chromatographic peak
Select the Manual Noise Region for the Genesis and ICIS Algorithms
Manually add, undo, and delete chromatographic peaks
Manually add Chromatographic peaks to the peak list
Import components from a processing method
Export a scan for a filtered chromatogram to a new raw data file
Work with sequences
Create a new sequence
Compare chromatogram traces in a sequence
Chromatogram–specific Toolbars
Chromatogram–Display Options toolbar
Display the Chromatogram - Display Options toolbar
Chromatogram–Workspace Processing toolbar
Peak Detection area
Tools Area
Sequence Toolbar
Sequence toolbar parameters
Chromatogram–Specific views
Chromatogram view
Chromatogram view shortcut menu commands
Chromatogram Ranges view
Chromatogram Ranges view parameters and icons
Use the Fill Down feature
Move a row
Delete rows
Peaks List view
Peaks List view parameters
Chromatogram–specific pages in the Info Bar
Detector Type page
Trace Type page
Scan Filters page
Scan Filters page parameters
Peak Detection page
Genesis Peak Detection Page
Genesis Peak Detection parameters
ICIS Peak Detection page
Display the ICIS peak detection parameters
ICIS Peak Detection page parameters
ICIS Signal-to-noise estimation
Avalon Peak Detection page
Avalon Peak Detection page parameters
PPD Peak Detection page
Display the PPD Peak Detection page
Sequence File page
Review spectral data
Display the scan corresponding to a particular time point in a chromatogram
Add Spectrum views to the workspace
Select Spectra from the Spectrum Ranges dialog box
Create a MultiSpectrum view and changing its Spectrum plots
Change a Spectrum view to a MultiSpectrum view
Format a MultiSpectrum view
Link and release Spectra to and from a Chromatogram
Linkage states for a Spectrum plot
Release a linked Spectrum from the Chromatogram
Link a spectrum view to a chromatogram
Averag a Spectra
Create an Average Spectrum from the Chromatogram shortcut menu
Create an Average Spectrum from the Spectrum Ranges dialog box
Subtract Background Spectra
Use the tools commands to subtract background spectra
Use the Spectrum Ranges Dialog box to subtract background spectra
Export a selected spectrum to a new raw data file
Use Precursor Markers to open data-dependent scans
Use the Precursor Flag marker
Use the Nearby Precursors marker
Specify the display options for the fragmentation scans
Select Spectra from an MSn Tree
Display the MSn Browser page
Display all the individual scan items
Specify the Display Options for a Spectrum view
Modify the scan header for the Spectrum view
Apply Local or Global Normalization in a MultiSpectrum view
Label Spectrum Peaks
Label APD Data in Spectrum Peaks
Add or remove the APD-specific labels
Label Mass Spectrum Peaks with Chemical Formulas
Add formula labels to the mass peaks in a spectrum plot
Change the y-axis scale of a Spectrum view
Change the zoom level in a Spectrum view or MultiSpectrum view
Spectra–specific Toolbars
Spectrum—Workspace Processing Toolbar
Spectrum—Workspace Processing commands
Spectrum—Display Options Toolbar
Spectrum—Display Options toolbar commands
MultiSpectrum—Display Options Toolbar
Spectra—specific views
Spectrum view
Add a Spectrum view to the Workspace
Spectrum (or MultiSpectrum) view shortcut menu
MultiSpectrum view
Spectrum Ranges dialog box
MSn Browser page
Review Map Data
Work with the Map view
Add Map views to the Workspace
Display the scan corresponding to a specific time point in Map view
Link and release Map to and from a Chromatogram
Link status of a Map view
Release a linked Map view from the Chromatogram
Link a map to a chromatogram
Change the Zoom level of a Map view
Use the Zoom Options toolbar
Map view—specific toolbars
Map view–Workspace Options toolbar
Map View–Display Options toolbar
Map View–Display Options toolbar icons
Map–Specific views
Map Ranges Dialog box
Map Ranges Dialog box parameters
Set Map Ranges
Define the Retention Time and Mass Ranges
Save a Map view
Set the Map Display Options
Set the Format Options
Style options
Set the map axis options
Set the map color options
Set the Band Width
Define the band width in a map view
Analyze MS Data using Data Analytics view
Add a Data Analytics view to the workspace
Plot the data as a Histogram
Plot the data in a Trend Chart
Data Analytics view—Specific toolbars
Data Analytics view–Workspace Options Toolbar
Display the Data Analytics view–specific Workspace Options toolbar
Data Analytics View–Display Options Toolbar
Display the Data Analytics View–Display Options toolbar
Save a Data Analytics plot
Data Analytics Ranges
Filter Data Analytics views by Trace types
Use the Status Trace type
Use Trailer Extra Information
Use Custom Trace Type
Create a Data Analytics plot
Determine the Elemental Composition of ions
Overview of an Elemental Composition Analysis
Start an elemental composition analysis
Use the fragments matching algorithm for Confirmation
Review the Elemental Composition Results
Review the best-matching formulas
Intensity Tolerances
Review the MS/MS coverage score for matching fragments
Review the MS/MS annotation results
Modify the elements in the Elements in Use Table
Add elements to the Elements in Use Table
Remove an element from the Elements In Use Table
Use custom periodic table for analysis
Add custom isotope abundance
Elemental Composition Results View
Simple Elemental Composition results view
Export simple elemental composition results as a CSV file
Elemental Composition page
Search Mass Spectrum Libraries
Performe a local NIST or mzVault Library Search
Set up the default Library Search parameters
Select the query Spectrum
Start a Library Search
Review the results of a local NIST or mzVault Library Search
NIST search results view
Review the Results of an mzVault Search
mzVault Search results view
Modify the settings for a local NIST or mzVault Library Search
Modify a NIST Search from the NIST Search page
NIST Search page parameters
Modify an mzVault Search from the mzVault Search page
mzVault Search page parameters
Search the online mzCloud mass spectral database
Export a Mass Spectrum to the NIST MS Search application
Manage Libraries
Add a library
Copy a library for archiving
Delete a selected library in the NIST Libraries list
Spectrum Workspace Processing Toolbar – Library Search features
Spectrum Workspace Processing Toolbar parameters
Simulate Isotope Distributions
Simulate the isotope distribution for a chemical formula or peptide
Display isotope simulations
Display Centroid and Profile Spectra in the same window
View both simulation types in the Isotope Simulation window
Isotope Simulation page
Work with CV plots for FAIMS data
Select the traces for display in the CV Plot view
CV Plot view
Export CV data to a file
Peptide Fragment Annotation
Overview of peptide fragments
Fragmentation methods
Annotate peptide fragments
Apply an amino acid sequence to a fragmented spectra
Display the Peptide Fragments page
Parameters for the Peptide Fragments page
Peptide Results view
Display or hide the Peptide Fragments table
Fragment ion series
Filter the Fragmented ions
View experiment and instrument information
Manage the Workspace Options toolbar – Report Area
Spectrum List – Display Options Toolbar
Display the Spectrum List – Display Options toolbar
Manage the Scan Header view
Manage the Spectrum List view
Manage the Status Log view
Manage the Instrument Method view
Manage the Tune Method view
Manage the Sample Information view
Manage the File Header view
Edit the File Header values
Heading Editor
Manage the Error Log view
Run the Xtract algorithm on Spectra and Chromatogram Data
Understand the Xtract algorithm
Apply the Xtract algorithm to an isotopically resolved spectrum
Display the Xtract page for a selected Spectrum
Xtract page parameters for a spectrum
Deconvolved Spectrum view
Run the Xtract algorithm and display the Deconvolved Spectrum view
Xtract Results view
Run the Xtract algorithm and display the Xtract Results view
Xtract Results view parameters
Expanded Xtract Results view parameters
Apply the Xtract algorithm to a chromatogram
Display the Xtract page for a chromatogram
Xtract Page for a Selected Chromatogram
FreeStyle default settings
Modify, Save, and Reset the default configuration options
Display the Default Mass Precision page
Default Mass Precision page parameters
Display the Default Peak Detection Algorithm page
Display the Default Number of Recently Used Files page
Default number of recently used files page parameter and buttons
Display the Default Raw Data Files Directory page
Default Raw Files Directory page parameter
Display the Default Elemental Composition Search Parameter page
Display the Factory Default Template page
Use the Default Library Search Parameters pages
Display the Workspace Options page
Workspace Options page parameters
Display the Xtract Options page
Default parameters for the Xtract algorithm
Scan Filters and Scan Headers
Scan Filter parameters
Display the Scan Header dialog box
Scan Headers and Scan Header abbreviations
One- and Three-Letter Abbreviations for Amino Acid Residues
Common Isotopes
Legal notices
Copyright and Trademarks
Compliance information

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