Create oligonucleotide sequences - BioPharma Finder Software - Intact Mass Analysis User Guide - Create oligonucleotide sequences - BioPharma Finder Software - BioPharma Finder Software

Intact Mass Analysis User Guide
Product Tree
Ardia Platform > Software > BioPharma Finder Software
Desktop Software > BioPharma Finder Software
Document Type
User Guide
Software version
5.3
  • 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
  • Stop/pause and resume the run queue
  • Remove jobs from the run queue
  • Queue page commands
  • 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
  • Create oligonucleotide sequences
  • Manually create a new oligonucleotide sequence
  • Import a FASTA file containing an oligonucleotide sequence
  • Create a mass-only or formula-only oligonucleotide sequence
  • Use the Random Sequence Generator
  • Specify oligo building blocks
  • Create custom oligo building blocks
  • Assign modifications to an oligonucleotide sequence
  • Create custom variable modifications
  • Assign Variable Modifications pane parameters and commands
  • Define default modifications for oligonucleotide sequences
  • Define Modification List table information
  • Default sublist of modifications for quick-loading
  • Save an oligonucleotide sequence
  • Oligonucleotide Sequence Editor parameters and commands
  • Oligonucleotide building block letter codes
  • Intact Mass Analysis features
  • Deconvolution algorithms
  • Xtract algorithm
  • ReSpect algorithm
  • Quality score algorithm
  • Best results with the ReSpect algorithm
  • Sliding Windows deconvolution
  • Processing modes: Automatic or Manual
  • Run an Intact Mass Analysis experiment
  • Work with an Intact Mass Analysis processing method
  • Default processing methods for Intact Mass Analysis
  • Component Detection parameters
  • Chromatogram Parameters area parameters
  • Source Spectra Method area parameters
  • ReSpect deconvolution parameters
  • Xtract deconvolution parameters
  • Plots on the Component Detection page
  • Identification parameters
  • Sequences for target matching experiments
  • Report parameters
  • Save Method page
  • Process an experiment in Manual mode
  • View Intact Mass Analysis results
  • Use real-time optimization (RTO) to reprocess results
  • Process and Review page
  • 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
  • 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
  • Report page
  • 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
  • Add or remove deconvoluted spectra to the Library
  • Compare deconvoluted spectra
  • Spectra Comparison page parameters
  • Mirror Plot pane 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

From the Sequence Manager, you can open the Oligonucleotide Sequence Editor to create a new sequence or edit an existing sequence.

In the Oligonucleotide Sequence Editor, you can add a new sequence by entering the sequence manually or importing a FASTA file. Additionally, you can assign a variety of default and custom modifications to the sequence and generate randomized sequence variations to include in the analysis before saving the sequence.

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