Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2017
peer-reviewed · Journal of the American Society for Mass Spectrometry · 2017. K. Ilker Sen et al. Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new…
| Date | 2017-05-01 |
| Type | peer-reviewed |
| Venue | Journal of the American Society for Mass Spectrometry |
| Publisher | American Chemical Society (ACS) |
| Contribution | algorithm |
| DOI | 10.1007/s13361-016-1580-0 |
| Citations (OpenAlex) | 46 |
| Venue 2-year citedness | 2.84 |
Abstract
Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests. Graphical Abstract ᅟ.
Methods and tools
- Supernovo: Automated antibody de novo sequencing: finds the closest-matching germline V-J-C sequences by database search, then converges on the true heavy and light chains by iterative wildcard substitution against the MS/MS spectra. Commercial, shipped in Protein Metrics’ Byos platform.
Cites (13)
- De Novo Sequencing and Resurrection of a Human Astrovirus-Neutralizing Antibody (2016) both
- Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies (2016) both
- Novor: Real-Time Peptide de Novo Sequencing Software (2015) both
- A Quantitative Tool to Distinguish Isobaric Leucine and Isoleucine Residues for Mass Spectrometry-Based De Novo Monoclonal Antibody Sequencing (2014) both
- Constrained De Novo Sequencing of Conotoxins (2012) both
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) both
- Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database (2010) both
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
- Automated de novo protein sequencing of monoclonal antibodies (2008) both
- Lookup Peaks: A Hybrid of de Novo Sequencing and Database Search for Protein Identification by Tandem Mass Spectrometry (2007) both
- De novo proteomic sequencing of a monoclonal antibody raised against OX40 ligand (2006) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) both
Cited by (27)
- XA-Novo: an accurate and high-throughput mass spectrometry-based de novo sequencing technology for monoclonal antibodies and antibody mixtures (2026) both
- Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle–Down, and De Novo Bottom–Up Mass Spectrometry (2025) both
- Homo-Tag-Assembler Assay for Full-Length Antibody Sequencing (2025) crossref
- Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry (2025) crossref
- Epitope and Paratope Mapping of a SUMO-Remnant Antibody Using Cross-Linking Mass Spectrometry and Molecular Docking (2025) both
- Decoding Protein Glycosylation by an Integrative Mass Spectrometry-Based De Novo Sequencing Strategy (2025) both
- Simplified and Rapid Workflow Enhances Throughput of De Novo Sequencing of COVID-19 Neutralizing Antibodies (2024) crossref
- A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics (2024) both
- Into the Dark Serum Proteome: Personalized Features of IgG1 and IgA1 Repertoires in Severe COVID-19 Patients (2024) both
- Antibody proteomics (2023) crossref
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly (2023) both
- A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies (2022) both
- No patient is the same; lessons learned from antibody repertoire profiling in hospitalized severe COVID-19 patients (2022) both
- De novo assisted AFB1-Specific monoclonal antibody sequence assembly and comprehensive molecular characterization (2022) crossref
- Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling (2022) both
- Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies (2022) both
- Template-Assisted De Novo Sequencing of SARS-CoV-2 and Influenza Monoclonal Antibodies by Mass Spectrometry (2022) crossref
- Template-based assembly of proteomic short reads for de novo antibody sequencing and repertoire profiling (2022) crossref
- Use of PASEF for Accelerated Protein Sequence Confirmation and De Novo Sequencing with High Data Quality (2022) crossref
- Human plasma IgG1 repertoires are simple, unique, and dynamic (2021) both
- De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma (2021) both
- Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme (2021) both
- Mass spectrometry-based de novo sequencing of the anti-FLAG-M2 antibody using multiple proteases and a dual fragmentation scheme (2021) both
- Selectivity over coverage in de novo sequencing of IgGs (2020) both
- Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
- Lys-Sequencer: An algorithm for de novo sequencing of peptides by paired single residue transposed Lys-C and Lys-N digestion coupled with high-resolution mass spectrometry (2020) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref