Automated de novo protein sequencing of monoclonal antibodies

peer-reviewed · Nature Biotechnology · 2008

peer-reviewed · Nature Biotechnology · 2008. Nuno Bandeira et al.

Date	2008-12-01
Type	peer-reviewed
Venue	Nature Biotechnology
Publisher	Springer Nature
Contribution	downstream-application
DOI	10.1038/nbt1208-1336
Citations (OpenAlex)	140
Venue 2-year citedness	11.97

Authors

1. Nuno Bandeira · University of California San Diego
2. Vineet Pham · University of California San Diego
3. Pavel A. Pevzner · Max Planck Institute of Molecular Cell Biology and Genetics, University of California San Diego, University of Southern California
4. David Arnott · Genentech, Inc.
5. Jennie R. Lill · Genentech, Inc.

Methods and tools

• Automated mAb de novo (Bandeira SPS): Landmark Nat Biotech 2008 paper by Bandeira, Pham, Pevzner, Arnott & Lill: applies Shotgun Protein Sequencing (SPS), that is MS/MS spectral assembly, end-to-end to a monoclonal antibody, recovering both chains without any prior sequence.
• Shotgun Protein Sequencing: Assembly of overlapping tandem mass spectra for shotgun protein sequencing.

Cites (3)

• MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) 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 (17)

• Latent Imputation before Prediction: A New Computational Paradigm for De Novo Peptide Sequencing (2025) semanticscholar
• Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry (2025) crossref
• Highly Robust de Novo Full-Length Protein Sequencing (2021) both
• Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra (2021) both
• Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification (2020) crossref
• Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing (2018) crossref
• A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
• pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization (2017) crossref
• De novo peptide sequencing by deep learning (2017) crossref
• Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics (2017) crossref
• Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
• De Novo MS/MS Sequencing of Native Human Antibodies (2017) both
• Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013) both
• Shotgun Protein Sequencing with Meta-contig Assembly (2012) both
• Constrained De Novo Sequencing of Conotoxins (2012) both
• De Novo Sequencing and Homology Searching (2012) both
• Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref

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