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

BioPharma Finder 5.2 Oligonucleotide Analysis User Guide
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Document Type
User Guide
Software version
5.2
  • Oligonucleotide 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: Oligo
  • Import a workbook
  • Export a workbook
  • Delete a workbook
  • Edit an oligo workbook
  • Workbook Manager page parameters
  • Oligo Calculator and Workbook Editor Results table parameters
  • Simulated Spectrum and Predicted MS2 Spectrum pane commands
  • Using the Sequence Manager
  • Sequence Manager tasks
  • Sequence Manager page 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
  • Oligonucleotide analysis features
  • Experiment results display
  • Quantification of modifications
  • Use the Oligonucleotide Calculator and Workbook to generate theoretical results
  • Add theoretical sequences to the oligo workbook
  • Edit oligo workbook parameters
  • Oligonucleotide Calculator and Workbook commands and parameters
  • Running an oligonucleotide analysis
  • Data acquisition and nucleotide identification
  • Start a new oligonucleotide analysis experiment
  • Process an experiment on the Queue page
  • Batch and multiconsensus result formats
  • Working with an oligonucleotide processing method
  • Create or edit a processing method
  • Use the processing method editing wizard to edit parameters
  • Edit the Component Detection page
  • View and edit the signal threshold
  • Component Detection page layout and parameters
  • Edit the Identification page
  • Identification page layout and parameters
  • Edit the Customize Results page
  • Customize Results page layout and parameters
  • Edit the Save Method page
  • Viewing oligonucleotide 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
  • Predict MS2 spectra using the kinetic model
  • Viewing the Process and Review page for oligonucleotide analysis
  • View the Results tables
  • Change the reference condition
  • Export the Results table
  • Save an oligo workbook
  • Charge State Results/Consolidated Results for "Find All Masses" table parameters
  • Modification notation
  • Charge State Results for "Find All Masses" table parameters
  • 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 Oligo Match ID results
  • View the Trend Ratio plot
  • View the Trend MS Area plot
  • View the Fragment Coverage Map
  • View the oligonucleotide 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
  • Viewing the Coverage page for oligonucleotide analysis
  • 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 Oligonucleotide Sequence Coverage Map
  • Select Oligonucleotide Sequence Coverage Map components
  • Modify Oligonucleotide Sequence Coverage Map parameters
  • Coverage page parameters
  • Viewing the Modification Summary page for oligonucleotide analysis
  • 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
  • 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
  • References
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