BioPharma Finder Software

Significance of the Topic

Comprehensive characterization of biotherapeutics is critical for ensuring safety, efficacy, and regulatory compliance in pharmaceutical development.
The complexity of biologic molecules such as proteins, antibodies, oligonucleotides, and mRNA requires advanced analytical workflows to detect low-level variants, modifications, and impurities.
High-resolution accurate-mass (HRAM) LC-MS combined with automated data processing accelerates decision making and supports quality control throughout the biopharma pipeline.

Objectives and Overview of the Application Note

This application note presents the capabilities of Thermo Scientific BioPharma Finder software for end-to-end biotherapeutic analysis.
It demonstrates how workflow-driven tools streamline peptide mapping, host cell protein (HCP) quantitation, multi-attribute method (MAM) development, oligonucleotide sequencing, intact mass measurement, top-down proteoform identification, and hydrogen deuterium exchange (HDX) analysis.
Key goals include reducing manual steps, enhancing confidence in identifications, and enabling high-throughput processing.

Methodology and Workflow

BioPharma Finder software provides predefined and customizable workflows:

• Peptide mapping with MS and MS2 data for full sequence coverage and PTM identification
• HCP analysis using database searches against CHO, human, or custom proteomes
• MAM method development for monitoring process and product quality attributes (PQA/CQA)
• Oligonucleotide and mRNA mapping with in silico digestion, custom building blocks, and kinetic fragmentation prediction
• Intact and subunit mass deconvolution via Sliding Window, Xtract, and ReSpect algorithms
• Top-down proteoform analysis including variable site-specific modifications
• Automated HDX protection factor calculation for conformational assessment

Used Instrumentation

• Thermo Scientific Orbitrap mass spectrometers (e.g., Q Exactive UHMR)
• Electrospray ionization (ESI) sources
• Thermo Scientific Chromeleon Chromatography Data System (CDS) software
• Thermo Scientific ProSightPC software for top-down searches
• Sliding Window, Xtract, and ReSpect deconvolution algorithms

Main Results and Discussion

• Peptide mapping workflows delivered 100% sequence coverage, detected low-abundance PTMs and sequence variants, and enabled automated comparative batch analysis.
• HCP analysis identified and quantified process-related impurities with integrated quantitation profiles before and after purification.
• MAM workflows supported high-throughput monitoring of critical quality attributes and seamless export to Chromeleon CDS for compliant tracking.
• Oligonucleotide sequencing using a kinetic fragmentation model improved MS2 fragment matching confidence and facilitated identification of truncated species and variable modifications.
• Intact mass analysis accurately deconvoluted coeluting components, determined drug-to-antibody ratios (DARs), and detected mass differences down to a few daltons.
• Top-down proteoform searches characterized multiple variable site modifications and provided interactive fragment coverage maps.
• HDX protection factor plots enabled rapid conformational comparisons across batches of antibody subunits.

Benefits and Practical Applications

• Streamlined data workflows accelerate time to results and reduce hands-on effort.
• Flexible workflows and algorithm selection accommodate simple to complex samples.
• High-confidence identifications support critical decision making in R&D, QA/QC, and process development.
• Integrated visualization tools simplify detection of impurities, PTM trends, and structural changes.
• Export capabilities ensure compliance and facilitate transfer of PQA/CQA methods.

Future Trends and Opportunities

• Integration of machine learning for automated parameter optimization and anomaly detection.
• Expansion of native MS and coupling with ion mobility for advanced structural characterization.
• Cloud-based collaborative platforms for centralized data management and remote access.
• Enhanced multi-omic integration combining proteomics, glycomics, and oligonucleotide analytics.
• Real-time monitoring and adaptive workflows for continuous bioprocessing applications.

Conclusion

Thermo Scientific BioPharma Finder software offers a comprehensive, workflow-driven solution for biotherapeutic characterization.
Its automated data processing, high-confidence deconvolution algorithms, and integrated visualization tools enable rapid and accurate analysis of peptides, proteins, oligonucleotides, and more.
These capabilities support robust quality control, method development, and regulatory compliance in the biopharma industry.

Reference

No external references were provided in the source document.