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Peptide Mapping Analysis User Guide
Product Tree
Ardia Platform > Software > BioPharma Finder Software
Desktop Software > BioPharma Finder Software
Document Type
User Guide
Software version
5.4
  • BioPharma Finder
  • Getting started
  • About BioPharma Finder
  • New in this version
  • Special notices
  • Contact us
  • Data acquisition and component identification
  • Supported fragmentation methods
  • Start the application
  • Connect to the Ardia Platform
  • Register with the Ardia Platform
  • Sign in to your Ardia Platform account
  • Ardia Platform management
  • Results from earlier BioPharma Finder software versions
  • View, revert, and compare experiment versions
  • Exit the application
  • Data backup and recovery
  • Create or restore a database Snapshot
  • Manual database backup
  • Data space optimization
  • Create a new experiment
  • Start and name an experiment
  • Select raw data files
  • Add raw data files
  • Delete raw data files
  • Specify conditions
  • Result formats: Batch Processing and Multiconsensus
  • Select sequences
  • Select a processing method
  • Specify a processing method
  • Import a processing method
  • Export a processing method
  • Delete a processing method
  • Automatic parameter values
  • Use the run queue
  • Queue manipulation
  • Run queue table information
  • Open results
  • Organize experiment results on the Load Results page
  • Manage experiments in the Master List
  • Organize folders and experiments in the Working List
  • Introduction to BioPharma Finder workbooks
  • Manage workbooks
  • Workbook Manager commands
  • Workbook Manager table information
  • Create a target peptide workbook
  • Save experiment results to a target peptide workbook
  • Add theoretical components to a target peptide workbook
  • Specify target peptide workbook parameters
  • Peptide Workbook Editor Results table information
  • Peptide Workbook Editor commands
  • Create an oligo workbook
  • Save experiment results to an oligo workbook
  • Add theoretical sequences to an oligo workbook
  • Manually add sequences
  • Use a CSV file to add sequences
  • Specify oligo workbook parameters
  • Oligonucleotide Calculator and Workbook Editor Results table information
  • Oligonucleotide Calculator and Workbook Editor commands
  • Create an intact workbook
  • Save experiment results to an intact workbook
  • Intact Workbook Editor Results table information
  • Intact Workbook Editor commands
  • Use the Sequence Manager
  • Sequence Manager tasks
  • Sequence Manager table information
  • Using the Host Cell Protein Database Manager
  • Using the Theoretical Protein/Peptide Manager
  • Create or import a protein sequence
  • Specify digestion parameters
  • Add/edit target m/z parameters
  • Add/edit modifications
  • Generate and save theoretical components
  • Theoretical Protein/Peptide Manager Results table information
  • Theoretical Protein/Peptide Manager commands
  • Create protein sequences
  • Manually create a new protein sequence
  • Import a FASTA file containing a protein sequence
  • Assign modifications to a protein sequence
  • Manage disulfide links
  • Disulfide Link Definitions table information
  • Manage static modifications
  • Residue Properties and Modifications dialog box parameters and commands
  • Manage glycosylations
  • Manage variable modifications
  • Variable Modifications for Intact and Peptide Analysis pane parameters and commands
  • Define default modifications for protein sequences
  • Define Modification List table information
  • Default sublist of modifications for quick-loading
  • Create custom variable modifications
  • Modification Editor pane parameters and commands
  • Manage proteoforms
  • All Possible Proteoforms table information
  • Save a protein sequence
  • Protein Sequence Editor parameters and commands
  • Amino acid letter codes
  • Peptide Mapping Analysis features
  • Peptide Mapping Analysis workflows
  • Run a Peptide Mapping Analysis experiment
  • Hydrogen deuterium exchange (HDX) experiments
  • HDX sample preparation and data collection
  • Run an HDX experiment
  • HDX experiment output files
  • Work with a Peptide Mapping Analysis processing method
  • Component Detection parameters
  • Identification parameters
  • Host Cell Protein parameters
  • Hydrogen Deuterium Exchange parameters
  • Customize Results parameters
  • Save Method page
  • View Peptide Mapping Analysis results
  • Use real-time optimization (RTO) to reprocess results
  • Process and Review page
  • View the Results tables
  • Change the reference condition
  • Export the Results table
  • Charge State Results table parameters
  • Modification notation
  • Theoretical Digestion Results table parameters
  • Results table commands
  • View the chromatograms
  • Chromatogram plot types
  • Display multiple chromatogram plot types for a single raw data file
  • Display a single chromatogram plot type for multiple raw data files
  • Chromatogram pane commands
  • Manual integration of component peaks
  • View Peptide Match ID results
  • Interpret disulfide bonds
  • View the Trend Ratio plot
  • View the Trend MS Area plot
  • View the Fragment Coverage Map
  • View the protein sequence
  • View the deconvoluted and full-scan MS spectra
  • Full Scan Spectra pane commands
  • View the predicted and experimental MS/MS spectra
  • Compare experimental MS/MS spectra
  • Fragment ion types and colors
  • MS2 Spectra pane commands
  • Process and Review page parameters
  • Process and Review page commands
  • Identify components using de novo sequencing
  • Define amino acids for de novo sequencing
  • Predict MS/MS spectra using the kinetic model
  • Mapping > Coverage page
  • View the Coverage Results table
  • Export the Coverage Results table data
  • Coverage Results table parameters
  • Coverage Results table commands
  • View the Coverage chromatogram
  • Modify the shading parameters
  • Coverage Chromatogram pane commands
  • View the Sequence Coverage Map
  • Select Sequence Coverage Map components
  • Modify Sequence Coverage Map parameters
  • Coverage page parameters
  • Mapping > Modification Summary page
  • View the Modification Results table
  • Modify Modification Results parameters
  • Export the Modification Results table data
  • Upper section of Modification Results table parameters
  • Lower section of Modification Results table parameters
  • Modification Results table commands
  • View the Modification Components table
  • Change the percent abundance calculation
  • Export the Components table data
  • Components table commands
  • View the Modification plot
  • Modification Summary page parameters
  • Mapping > Host Cell Protein Quantitation page
  • View the Host Cell Protein Quantitation Results table
  • Export the Host Cell Protein Quantitation Results table data
  • Host Cell Protein Quantitation Results table parameters
  • Host Cell Protein Quantitation Results table commands
  • View the Host Cell Protein Quantitation Components table
  • Change the MS area calculation
  • Export the Components table data
  • Components table commands
  • View the Host Cell Protein Relative Quantitation plot
  • Host Cell Protein Quantitation page parameters
  • View host cell protein (HCP) experiment results
  • Mapping > Hydrogen Deuterium Exchange page
  • View hydrogen deuterium exchange (HDX) experiment results
  • HDX protection factor plot commands
  • Reporting
  • Add default BioPharma Finder report templates to the Ardia Platform data repository
  • Download default BioPharma Finder report templates
  • Create a folder in the Ardia Platform data repository for default report templates
  • Upload default report templates to the Ardia Platform data repository
  • Start a report
  • Report: Design page navigation
  • Insert a new sheet
  • Insert a report table
  • Insert a report plot
  • Insert a report variable
  • Insert a sequence coverage map
  • Report element sourcing
  • Use the Autorepeat feature
  • Report: Preview page navigation
  • Save a report
  • Reference information
  • Data conversion from legacy applications
  • Converted sequences
  • Converted processing methods
  • Appendix: Handling errors
  • Database service errors
  • Other errors
  • Appendix: Interactive functions
  • Copy and paste functions
  • Copy all contents in a pane
  • Copy a portion of contents in a pane
  • Organize panes
  • Basic chromatogram functions
  • Basic spectrum functions
  • Basic table functions
  • Sort rows
  • Show or hide columns
  • Filter data in a table
  • Filter data rows
  • Table filter operators
  • Table filter operands
  • Create, save, and apply custom filters
  • Remove filters
  • Save filters to a file
  • Apply saved filters to data
  • Appendix: Glycans
  • N-linked glycans in the Define Modification List window
  • N-linked glycans with a CHO host cell-line type
  • N-linked glycans with a human host cell-line type
  • O-linked glycans
  • References
  • Copyright Information

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