Sequences Information section - Sequences Information section - BioPharma Finder 5.2 Intact Mass Analysis User Guide - BioPharma Finder Software - Sequences Information section - BioPharma Finder Software - BioPharma Finder Software - topic

BioPharma Finder 5.2 Intact Mass Analysis User Guide
Product Tree
Ardia Platform > Software > BioPharma Finder Software
Desktop Software > BioPharma Finder Software
Document Type
User Guide
Software version
5.2
  • Intact Mass 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
  • Use a Chromeleon-compatible workbook: Intact
  • Import a workbook
  • Export a workbook
  • Delete a workbook
  • Edit an intact workbook
  • Workbook Manager page parameters
  • Workbook Editor page parameters
  • 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
  • Creating and managing oligonucleotide sequences
  • Create and edit oligonucleotide sequences
  • Import a FASTA file containing an oligonucleotide sequence
  • Manually create a new oligonucleotide sequence
  • Select the experiment category for a sequence
  • Create a mass-only or formula-only oligonucleotide sequence for intact mass analysis
  • Use the Random Sequence Generator for oligonucleotides
  • Change the default modifications for oligonucleotide sequences
  • Define default modifications for oligonucleotide sequences
  • Default sublist of modifications for quick loading
  • Assign custom building blocks to an oligonucleotide sequence
  • Manage variable modifications
  • Assign variable modifications
  • Assign Variable Modifications pane parameters
  • Manage custom modifications and building blocks for oligonucleotides
  • Add custom modifications
  • Add custom building blocks
  • Edit custom modifications or oligo building blocks
  • Delete custom modifications or oligo building blocks
  • Save an oligonucleotide sequence
  • Save an oligonucleotide sequence under the same name (overwrite)
  • Save an oligonucleotide sequence under a new name
  • Oligonucleotide Sequence Editor parameters
  • Intact mass analysis features
  • Deconvolution algorithms
  • Xtract algorithm
  • ReSpect algorithm
  • Quality score algorithm
  • Best results with the ReSpect algorithm
  • Sliding windows deconvolution
  • Processing modes: Manual vs. Automatic
  • Target sequence matching
  • Extracted ion chromatogram (XIC) generation
  • Abundance traces
  • Drug-to-antibody ratio (DAR) values
  • Spectral comparison
  • Running an intact mass analysis
  • Start a new intact mass analysis experiment: Manual mode
  • Process an experiment in Manual mode
  • Start a new intact mass analysis experiment: Automatic mode
  • Process an experiment on the Queue page (Automatic mode)
  • Batch and multiconsensus result formats
  • Working with an intact mass processing method
  • Create or edit a processing method
  • Default processing methods for intact mass analysis
  • Use the processing method editing wizard to edit parameters
  • Edit the Component Detection page
  • Specify parameters on the Component Detection page
  • Chromatogram Parameters area parameters
  • Source Spectra Method area parameters
  • ReSpect deconvolution parameters
  • Xtract deconvolution parameters
  • Plots on the Component Detection page
  • Component detection page commands
  • Edit the Identification page
  • Sequences for target matching experiments
  • Identification page parameters
  • Identification page tables
  • Edit the Report page
  • Report page parameters
  • Edit the Save Method page
  • Viewing intact mass 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
  • Reporting page: View a deconvolution report
  • Report sections
  • Sample Information section
  • Chromatogram Parameters section
  • Chromatogram section
  • Main Parameters section
  • Advanced Parameters section
  • Source Spectra Parameters section
  • Sequences Information section
  • Source Spectrum section
  • Deconvoluted Spectrum section
  • ReSpect/Xtract Masses Table section
  • Component Details Tables section
  • Source Spectrum Evidence Plot section
  • Reporting page toolbar
  • Spectra Comparison page: Compare deconvoluted spectra
  • Add or remove deconvoluted spectra to the Library
  • Compare deconvoluted spectra
  • Spectra Comparison page parameters
  • Mirror Plot pane commands
  • Viewing the Process and Review page for intact mass analysis
  • View the Results table
  • Change the reference mass
  • Results table parameters (for single file or batch format experiments)
  • Results table parameters (multiconsensus format experiments)
  • Additional Results table parameters for target sequence matching experiments
  • Export the Results table
  • Save an intact workbook
  • Results table commands
  • View the chromatograms
  • Chromatogram plot types
  • Chromatogram pane commands
  • View the deconvoluted spectra
  • Deconvoluted Spectrum pane commands
  • View the source spectra
  • Source Spectrum pane commands
  • View the matched sequence information
  • Change the matched sequence identification for a component
  • Component Information table parameters
  • Target Match Sequence table parameters
  • View the average drug-to-antibody ratio (DAR) values
  • Average DAR table parameters
  • Component Specific Summary table parameters
  • Average DAR pane commands
  • 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

The Sequences Information section of a report, shown in the following figure, displays the sequence settings that you chose using the Sequence Editor, including modification and identification parameters, for each sequence used in the experiment. See Creating and managing protein sequences and Creating and managing oligonucleotide sequences.

Sequences Information section, shown for a intact protein experiment.
Sequences Information section, shown for a intact protein experiment.
Back to home page