MassHunter BioConfirm Software
Routine characterization of complex biomolecules through comprehensive workflows
- MassHunter BioConfirm software streamlines routine biomolecule characterization through comprehensive workflows. These include intact peptide purity, impurities, and sequencing, oligonucleotide impurity assessment and sequence confirmation, as well as intact protein analysis with peptide mapping and released glycan profiling. <br>As part of the Agilent comprehensive biopharma solution—from automated sample preparation to LC/TOF or LC/Q-TOF analysis, data evaluation, and reporting—this software provides tools such as protein deconvolution, drug-to-antibody ratio (DAR) calculator, report templates, and Agilent MassHunter WalkUp integration. Advanced security features and built-in technical controls help minimize risk and preserve data integrity.
- MassHunter BioConfirm software is part of the end-to-end solutions offered by Agilent for biopharma workflows, also including the Agilent AssayMAP Bravo protein sample prep platform, Agilent 1290 Infinity III bio LC, and Agilent LC/TOF and LC/Q-TOF systems, consumables, and services
- MassHunter WalkUp provides sample submitters access to expert LC/MS capabilities without requiring them to be experts in liquid chromatography/mass spectrometry
- Compatible with Agilent MassHunter Acquisition for LC/MS (all models) or Agilent OpenLab CDS 3.0 software (6230C, 6545XT, Revident)
- Compliance-ready features keep you in control - with e-signatures, advanced security capabilities, and built-in technical controls, BioConfirm software can minimize security risks while helping to preserve data integrity
- Sequence manager and Chemical Data Dictionary are now client/server capable
Comprehensive Biomolecule Characterization
Analysis of intact peptides and proteins, oligonucleotides, protein digests, and released glycans in a single software
Overview
Agilent LC/TOF
Agilent LC/Q-TOF
Features
Reduce complexity and increase productivity
Why BioConfirm is the preferred choice for biopharma workflows. Find out how it works
Intact peptides workflow – isotope deconvolution
Analyze intact peptide therapeutics with a resolved isotope deconvolution and matching workflow. Confirm the purity by conducting a relative quant calculation based on either MS-based or LC-based chromatographic signals.
Intact peptides workflow – sequence coverage and impurity analysis
Analyze intact peptide therapeutics and determine the sequence coverage for both the target molecule as well as any detected impurity in the sample.
Synthetic peptide analysis
Quality control of synthetic peptides requires the identification and determination of impurities, which can arise during production or storage. These include amino acid additions, insertions, deletions, truncations, oxidation, deamidation, and more, as well as fatty acid related impurities. Learn about Impurity Profiling of GLP-1 Receptor Agonists by HILIC-MS
BioConfirm and LC/MS
Quality control of synthetic peptides requires the identification and determination of impurities. The mass of the peptide can be accurately determined using LC/MS, and with MS/MS analysis, the sequence can be confirmed through the predicted fragmentation pattern. Discover LC/MS-Based Characterization of GLP-1 Therapeutic Peptide Liraglutide and Impurities
Protein digest workflow
For peptide mapping, confidently perform sequence confirmation and review multiple samples (for example, different digest enzymes) simultaneously using Sequence Coverage Map. View the biomolecule fragmentation spectrum with multicolored labeling for rapid confirmation of MS/MS fragmentation efficiency. Quickly assess digestion efficiency with your sequence coverage map.
Advanced peptide mapping algorithms
The peptide mapping algorithm uses MS/MS data to confirm the peptides. Results are displayed in a Sequence Coverage Map that allows you to review coverage and align multiple samples. In addition, fast disulfide bond mapping can be used to untangle the scrambling of disulfide bonds in a monoclonal antibody.
Histogram plots for comparisons
Histogram plots let you compare multiple PTMs or conditions such as quantitative glycopeptides analysis.
Intact protein analysis workflow
For intact protein analysis, rapidly deconvolute your intact protein data to determine molecular weights and confirm post-translational modifications (PTMs). Get a comprehensive list of your proteoforms in the biomolecule table. Easily view the spectra of multiple proteoforms with deconvoluted results in the deconvolution pane.
Antibody-drug conjugates (ADCs)
Drug-to-antibody ratio (DAR) is a key measure of antibody-drug conjugates (ADCs). BioConfirm includes a DAR Calculator to rapidly calculate DAR values for both intact and reduced ADCs with minimal user input. The DAR spectrum allows for inspection of the results and user-determined refinement of the calculations. Learn more about Agilent applications in ADC analysis.
Deconvolution for MW confirmation and glycoform detection
MassHunter BioConfirm deconvolutes intact protein mass spectrometry data to determine molecular weights and confirm glycoforms. They can be labeled on the mass spectrum and inspected by their relative quantitative amounts using tables or histogram plots.
Relative quantitation
MassHunter BioConfirm allows you to perform relative quantitation in its individual workflow, including predicted modifications in proteins, modified and unmodified peptides, and glycoforms. You can also compare multiple samples and view relative quantitation results from up to 10 data files in a histogram.
Oligonucleotide characterization workflow
Quickly set up impurity analysis and sequence confirmation workflows for oligonucleotide characterization using preferred definitions for building blocks, linkers, and modifications. View fragmentation spectrum with multicolored labeling for rapid confirmation of MS/MS fragmentation efficiency. View fragmentation ladder with multicolored labeling for rapid confirmation of sequence coverage.
Defining complex oligonucleotides
Sequence Manager allows customization of oligonucleotide building blocks, linkers, and modifications. You don’t have to adhere to a single syntax, giving you the flexibility to use the specific terminology that you want for your oligonucleotide analysis.
Oligo sequencing: Fragmentation ion nomenclature and accurate mass
The MS/MS fragmentation of oligos can be complex, and the main fragments produced can change depending on the nucleotide chemistry. BioConfirm can calculate all the fragments, match the ions to the fragmentation spectra, and provide visualizations for quick confirmation of sequence coverage.
Oligonucleotide sequence confirmation workflow
The automated data analysis workflow for Sequence Confirmation (SC) on MS/MS fragments is accomplished in minutes. Results are displayed in an easy-to-read fragment confirmation ladder visualization—providing complete and high-confidence coverage for short oligonucleotides from just one injection.
Oligonucleotide Target Plus Impurities workflow: User interface
Rapidly confirm the oligonucleotide product and profile its impurities using either untargeted deconvolution or targeted Agilent Find-by-Formula (FBF). Quickly visualize the target and impurities present in the sample using the deconvoluted spectrum and view the full list in the biomolecule table.
Oligonucleotide Target Plus Impurities workflow: Results table
The Target Plus Impurities (TPI) workflow uses oligonucleotide MS data to identify the full-length product (FLP) as well as any impurities. Find-by-Formula (FBF) or maximum entropy algorithms identify the target oligo and related truncation impurities.
Oligonucleotide Target Plus Impurities: Degradation product identification
Forced degradation studies serve as a critical tool for evaluating chemical stability and elucidating the degradation pathways of synthetic oligonucleotides. The Target Plus Impurities workflow can be used to identify degradation products, including truncated shortmers and oxidized degradants. Forced Degradation Studies of Synthetic Oligonucleotide
Released glycans profiling workflow
Identify released glycans using a curated database, accommodating commercial and custom tags, to profile glycan structure on proteins.
Glycoform identification
The intact protein workflow uses deconvolution to determine the glycoforms in the sample. The nonreduced sample condition provides rapid assessment of the major glycoforms of the intact mAb, while the reduced sample condition offers quantitative information about individual glycans such as G0F, G1F, and G2F. Learn more about Agilent tools for protein glycosylation analysis.
Released glycans analysis
The released glycans results include spectra annotated with the glycan structure and theoretical isotope distribution. The Find-by-Formula algorithm takes advantage of the tendency of glycans to ionize with multiple adducts, resulting in finding species such as M + H + Na and giving greater specificity. Learn more about the Agilent platform to facilitate N-glycan sample preparation.
Released glycan workflow supports custom labels
These labels for released glycan analysis are supported by BioConfirm: The commonly used commercial tags, 2-aminobenzamide (2-AB) and InstantPC, are available with default selection in the released glycans workflow. Users are also allowed to submit their own customized labels in the released glycans workflow. Learn more about Agilent applications for released glycans,
How it works
End-to-end workflow
Agilent MassHunter BioConfirm software is part of Agilent’s end-to-end biopharma workflows, providing solutions for biotherapeutic analysis and characterization. This biopharmaceutical software can process data from Agilent time-of-flight (TOF) and quadrupole time-of-flight (Q-TOF) LC/MS instruments.
BioConfirm streamlines the characterization of complex biomolecules with intuitive workflows for therapeutic peptides, oligonucleotides, intact proteins, peptide mapping, and released glycan analysis.
Customer stories
“BioConfirm has been a game changer. It helps us to automate impurity profiling across different oligo types, saving time and improving consistency.”
Dimas Echeverria
Director, Nucleic Acid Chemistry Center, UMass Chan Medical School
Turning Ideas into Therapeutic Realities
Applications
One unified interface for all your biocharacterization workflows
Intact peptides
Intact peptide workflows enable characterization of a new class of metabolic therapeutics, including synthetic peptides such as GLP-1 RAs. BioConfirm can define peptides containing nonnatural amino acids and long-side-chain modifications.
Capabilities include:
- MS/MS identification workflow for target and impurities
- MS Target Plus Impurities mass identifications with a new isotopically resolved deconvolution algorithm
Oligonucleotide analysis
Oligonucleotide therapeutics are being developed for a wide range of indications.
MassHunter BioConfirm software enables you to rapidly set up workflows for oligonucleotide characterization:
TPI uses oligonucleotide MS data to identify the full-length product (FLP) as well as any impurities. SC using MS/MS fragmentation is accomplished in minutes.
Intact protein analysis
Protein therapeutics, such as monoclonal antibodies (mAbs) and their derivative products, are a very important class of biopharmaceutical molecules. MassHunter BioConfirm analyzes intact protein mass spectrometry data using deconvolution to determine molecular weights and confirm posttranslational modifications (PTMs), for example glycoforms. A built-in drug-to-antibody ratio (DAR) calculator enables simple and automated calculations for antibody-drug conjugates (ADCs).
Peptide mapping
Peptide mapping is the most widely used analytical technique to confirm the identity of biotherapeutic proteins, including their primary amino acid sequence and structural characteristics (for example, PTMs, disulfide linkage information). The protein of interest is typically digested into smaller peptides through an enzymatic reaction, separated by LC, and detected by MS. MassHunter BioConfirm uses advanced peptide mapping algorithms to narrow the list of possible peptides, providing highly confident data and saving you manual inspection time.
Released glycan profiling
Consistent glycosylation of therapeutic mAbs is important in pharmaceutical bioprocessing. Released glycan profiling is an effective approach for glycan identification and quantitation.
The BioConfirm released glycans workflow is easy to set up and accommodates many commercial and custom tags (fluorescent labels). A curated glycan database is also available and can easily be extended with additional glycans.
Specifications
Workstation
Networked Workstation
Documents & support
MassHunter BioConfirm software
Step inside--click each hotspot to learn more about Sequence Manager. You can also navigate between the Sequence Manager screen and the Chemical Data Dictionary Editor screen
-
FASTA file import
Enables bulk import of sequences from .fasta file format for straightforward build of your sequence library.
-
Chemical data dictionary access
Easily access chemical data dictionary for defining custom sequence building blocks and modifications.
-
List of defined sequences
Your complete set of sequences organized by protein/peptides or oligonucleotides for easy access.
-
Sequence customization
Add modifications to sequences for customization of your molecule library. Allows positional fixed modifications from the chemical data dictionary..
- 5%, 15%
- 34%, 18%
- 15%, 35%
- 60%, 25%
-
Modification profiles
Customized groupings by molecule type allow you to group modifications without having to select them individually, for faster method setup.
-
Complete list of defined modifications
Complete list of modifications grouped by chemical type for organization and rapid look-up.
-
Defining custom modifications
Easily build custom modifications to define complicated biomolecules, enabling comprehensive characterization.
- 25%, 31%
- 50%, 55%
- 85%, 70%
Expert-led video resources
Frequently asked questions
Can MassHunter BioConfirm be used in an automated fashion?
Yes, MassHunter BioConfirm methods can run as part of a worklist from MassHunter acquisition or from MassHunter WalkUp software.
Can MassHunter BioConfirm support relative quantitation?
Yes, MassHunter BioConfirm allows you to do relative quantitation in its individual workflow, including predicted modifications in proteins, modified and unmodified peptides, and glycan contents. BioConfirm also allows multiple samples to be compared, with relative quantitation results from up to 10 different data files displayed in a histogram.
Which advanced security features and technical controls does MassHunter BioConfirm have?
In MassHunter BioConfirm, an administrator can configure projects, make user roles with permissions, and manage audit trails. For Networked Workstation installations, security policies are enforced, such as application lock and timeouts. All files are stored in secure content management systems with versions for data files, methods, protein sequences, reports, and report templates. Learn more about regulatory compliance for MassHunter software solutions and visit our Data Integrity Resource Center.
Can I integrate my UV chromatogram and identify what's underneath?
Yes. BioConfirm can integrate UV chromatograms and provide the identity of the eluting peak by mass spectrometry.
I am really interested in MassHunter BioConfirm, can I try it out?
Yes, MassHunter BioConfirm offers a 60-day trial period without a required license key. Please download MassHunter BioConfirm at Agilent SubscribeNet or contact your regional sales representative.
How can I integrate data from multiple runs into one report in MassHunter BioConfirm?
Oligonucleotide sequence analysis often requires several experimental runs (for example, fragmentation of different precursors) as well as optimization of collision energy. MassHunter BioConfirm can combine multiple sample acquisitions, maximize the sequence coverage of the target oligonucleotide, and generate a batch report detailing the combined sequence coverage. This capability is also available for peptide mapping data.
Can data analyzed in MassHunter BioConfirm be reviewed in batch format using BioMS Reviewer software?
Yes. Users can use the BioMS Reviewer to evaluate such data generated using MassHunter BioConfirm.
Is it possible to get upgrades to MassHunter BioConfirm when they release?
Yes, MassHunter BioConfirm comes with a Software Maintenance Agreement (SMA) that includes free upgrades while the SMA is active. Please register your product in Agilent SubscribeNet to receive notifications automatically.
style
Tools
A useful selection of resources
Protein modifications
UNIMOD is a community supported, public domain, comprehensive database of protein modifications for mass spectrometry (MS) applications.
Common ESI background ions
A list of common electrospray ionization (ESI) background ions curated by the University of Washington Proteomics Resource (UWPR) proteomics facility.
De novo peptide sequencing
A peptide sequencing tutorial created by the IonSource mass spectrometry educational resource.
Peptide mass calculator
The calculator operated by the SIB Swiss Institute of Bioinformatics cleaves a protein sequence and computes the masses of the generated peptides.
ESIprot Online: Mass deconvolution calculator
ESIprot Online enables charge state determination and molecular weight calculation for low-resolution ESI mass spectrometry protein data.
GlycReSoft software
Open-source and publicly available software for glycomics and glycoproteomics by Boston University School of Medicine.
Real-world expertise from the Agilent community
Q: How do I change deconvolution integration in BioConfirm 12.1?
A: Other than manual integration, you can try adjusting your deconvolution parameters, if possible, to produce data that integrates more favorably.
Training & events
Agilent University BioConfirm course catalog
Agilent University delivers training to build skills that you can put to work immediately. Learn the essentials of BioConfirm.
OpenLab CDS acquisition training
Video tutorials to get you started with OpenLab CDS.
Cloud-based help and learning for OpenLab CDS
Access OpenLab CDS learning materials from any device, anytime. Find up-to-date guides, manuals, and more when you need them.
Stay connected with Agilent live or recorded webinars
These free webinars are a convenient way to keep your technical knowledge up to date and learn from industry peers.
Meet us at these events for more educational opportunities
Information on local seminars and user group meetings as well as trade shows and conferences Agilent will be attending around the world.
Related products
PRDT_792793
PRDT_880477
PRDT_792798
PRDT_788136
PRDT_792866
PRDT_4586715
PRDT_788217
PRDT_788224
PRDT_3638459
PRDT_4603496
PRDT_788217
PRDT_788224
PRDT_3638459
PRDT_4603496
Software support and resources
Get support from our technical experts driving lab performance and reliability
World-class team of experts dedicated to you. Hand selected from across the globe, each bringing a wealth of experience and expertise to help you solve your issue quickly and efficiently.
Agilent University
Customized training and support for your lab. Agilent University offers in-person or virtual training courses and webinars.
Financial solutions
Learn about financing options through Agilent Financial Solutions to help you acquire the equipment you deserve.
OpenLab help & learning
A portal that has user guides on how to operate the software
Virtual tech support
Live technical help directly from experts using phone, video conferencing or the Virtual Assist app.
Software service desk
Submit a ticket to our service desk or login to see the status of your ticket
Agilent SubscribeNet
Manage and effectively operate your software licenses with SubscribeNet. Register today in just a few quick steps.