Creating and managing protein sequences - BioPharma Finder Software - Creating and managing protein sequences - BioPharma Finder Software - BioPharma Finder Software

BioPharma Finder 5.2 Top Down Analysis User Guide
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Desktop Software > BioPharma Finder Software
Ardia Platform > Software > BioPharma Finder Software
Document Type
User Guide
Software version
5.2
  • Top Down Analysis
  • Copyright Information
  • About the BioPharma Finder application and user guides
  • New to this version
  • Special notices
  • Access the documentation
  • View the user guides
  • View the glossary
  • Update the help system and user guides
  • Contact us
  • Getting started
  • Local mode
  • Ardia platform connection
  • Register with the Ardia platform
  • Sign in to your Ardia platform account
  • Results from earlier BioPharma Finder software versions
  • Ardia platform management
  • Disconnect from the Ardia platform
  • Lock the application
  • Unlock the application
  • Unlock the application as the last logged-in user
  • Unlock the application when the last logged-in user is not available
  • Data space optimization
  • Optimize disk space
  • Purge all BioPharma Finder files
  • Data backup and recovery
  • Create or restore a database Snapshot
  • Manual database backup
  • Exit the application
  • Common features for different analyses
  • Fragmentation methods
  • Create a new experiment
  • Select raw data files
  • Load raw data files
  • Change the location of a raw data file
  • Delete raw data files
  • Select one or more sequences
  • Select a processing method
  • Import a processing method
  • Export a processing method
  • Select a processing method
  • Delete a processing method
  • Save a processing method
  • View and export the Method Summary on the Save Method page
  • Save a processing method
  • Effects after saving the processing method
  • Use the run queue
  • Manage the run queue (except intact mass analysis)
  • Pause the run queue
  • Resume the paused queue
  • Remove jobs from the run queue
  • Manage the run queue for intact mass analysis
  • Pause the run queue
  • Resume the paused queue
  • Remove jobs from the run queue
  • Queue page parameters
  • Organize experiment results
  • Manage experiment results in the Master List
  • Manage folders and experiment results in the Working List
  • Using the Sequence Manager
  • Sequence Manager tasks
  • Sequence Manager page parameters
  • Creating and managing protein sequences
  • Create and edit protein sequences
  • Import a FASTA file containing a protein sequence
  • Manually create a new protein sequence
  • Select the experiment category for a sequence
  • Edit the amino acids in an existing protein sequence
  • Amino acid letter codes
  • Assigning modifications to a protein sequence
  • Order of modification assignments
  • Manage disulfide links
  • Assign disulfide links
  • Remove disulfide links
  • Disulfide Link Definitions pane parameters
  • Manage static modifications
  • Assign static modifications
  • Remove static modifications
  • Residue Properties and Modifications dialog box parameters
  • Manage glycosylations
  • Manage variable modifications
  • Assign variable modifications
  • Variable Modifications for Peptide Mapping Analysis/Intact Analysis pane parameters
  • Manage proteoforms
  • Define the modification list for proteoforms
  • Generate and save proteoforms
  • All Possible Proteoforms table
  • Change the default modifications for protein sequences
  • Define default modifications for protein sequences
  • Default sublist of modifications for quick loading
  • Manage custom modifications for protein sequences
  • Add custom modifications
  • Edit custom modifications
  • Delete custom modifications
  • Modification Editor pane parameters
  • Save a protein or peptide sequence
  • Save a protein or peptide sequence under the same name (overwrite)
  • Save a protein or peptide sequence under a new name
  • Protein Sequence Editor parameters
  • Using the Host Cell Protein (HCP) Database Manager
  • Add an HCP database
  • Delete an HCP database
  • Using the Theoretical Protein/Peptide Manager
  • Create or import a protein or peptide sequence
  • Specify digestion parameters
  • Add/edit target m/z parameters
  • Add/edit modifications
  • Save a peptide workbook
  • Results table parameters
  • Top down analysis features
  • Similarities to intact mass analysis
  • Spectral deconvolution for top down analysis
  • Running a top down analysis
  • Start a new top down analysis experiment
  • Process an experiment on the Queue page
  • Batch and multiconsensus result formats
  • Working with a top down processing method
  • Create or edit a processing method
  • Use the processing method editing wizard to edit parameters
  • Edit the Component Detection page
  • Peak Selection parameters
  • ReSpect deconvolution parameters
  • Xtract deconvolution parameters
  • Plots on the Component Detection page
  • Component Detection page commands
  • Edit the Identification page
  • Sequences for top down analysis experiments
  • Identification page parameters
  • Identification page tables
  • Edit the Save Experiment page
  • Viewing top down analysis results
  • Open results
  • Open results from the Queue page
  • Open results from the Load Results page
  • Use real-time optimization (RTO) to reprocess results
  • Viewing the Process and Review page for top down analysis
  • View the Results tables
  • Change the reference mass
  • Intact Fragmentation Results table parameters
  • Intact Deconvolution Results table parameters
  • Export the Results tables
  • Results tables commands
  • View the chromatograms
  • Chromatogram plot types
  • Chromatogram pane commands
  • View the deconvoluted spectra
  • Deconvoluted Spectrum panes commands
  • View the source spectra
  • Source Spectrum panes commands
  • View the ProSightBP Fragment Map
  • Matching Fragment Detail table parameters
  • ProSightBP Fragment Map pane commands
  • View the ProSightBP Output Results table
  • Export the ProSightBP Output Results table
  • ProSightBP Output Results table parameters
  • ProSightBP Output pane commands
  • View the matched sequence information
  • Change the matched sequence identification for a component
  • Component Information table parameters
  • Target Match Sequence table parameters
  • Process and Review page parameters
  • Process and Review page commands
  • 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
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