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 Science and Business Media LLC |
| Contribution | downstream-application |
| DOI | 10.1038/nbt1208-1336 |
| Citations (OpenAlex) | 133 |
| Venue 2-year citedness | 12.89 |
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.
Methods it uses
- Shotgun Protein Sequencing: Assembles overlapping MS/MS spectra of related peptides into contigs before any sequence is called, so a protein is sequenced from the assembly rather than from individual spectra. Tolerates mixtures and unanticipated modifications.
Cites (6)
- Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins (2007) both
- MSNovo: A Dynamic Programming Algorithm for de Novo Peptide Sequencing via Tandem Mass Spectrometry (2007) both
- Protein identification by spectral networks analysis (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 (59)
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- 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
- Decoding Protein Glycosylation by an Integrative Mass Spectrometry-Based De Novo Sequencing Strategy (2025) both
- De novo protein sequencing of antibodies for identification of neutralizing antibodies in human plasma post SARS-CoV-2 vaccination (2024) both
- A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics (2024) both
- de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination (2024) crossref
- A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies (2022) both
- Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling (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
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- Spectrum graph-based de-novo sequencing algorithm MaxNovo achieves high peptide identification rates in collisional dissociation MS/MS spectra (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
- Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics (2019) both
- 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
- Protein de novo sequencing by top-down and middle-down MS/MS: Limitations imposed by mass measurement accuracy and gaps in sequence coverage (2018) crossref
- De Novo Sequencing of Proteins and Peptides: Algorithms, Applications, Perspectives (2018) crossref
- pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization (2017) crossref
- Antibody de novo Sequencing (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
- Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination (2017) both
- Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery (2017) both
- Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? (2017) crossref
- Filling a Protein Scaffold With a Reference (2017) crossref
- De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence (2017) both
- Ultrahigh‐resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven‐protein mixture by paired single‐residue transposed Lys‐N and Lys‐C digestion (2017) crossref
- De Novo MS/MS Sequencing of Native Human Antibodies (2017) both
- Rapid Distinction of Leucine and Isoleucine in Monoclonal Antibodies Using Nanoflow LCMSn (2017) crossref
- Peptidomics of Acanthoscurria gomesiana spider venom reveals new toxins with potential antimicrobial activity (2017) crossref
- De novo Peptide Sequencing (2016) crossref
- Top-down analysis of protein samples by de novo sequencing techniques (2016) crossref
- Complete De Novo Assembly of Monoclonal Antibody Sequences (2016) both
- Filling a Protein Scaffold with a Reference (2016) both
- Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies (2016) both
- De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra (2015) crossref
- De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014) crossref
- A Quantitative Tool to Distinguish Isobaric Leucine and Isoleucine Residues for Mass Spectrometry-Based De Novo Monoclonal Antibody Sequencing (2014) crossref
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013) both
- High-definition De Novo Sequencing of Crustacean Hyperglycemic Hormone (CHH)-family Neuropeptides (2012) both
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- The spectral networks paradigm in high throughput mass spectrometry (2012) both
- Primary sequence determination of a monoclonal antibody against α-synuclein using a novel mass spectrometry-based approach (2012) crossref
- De Novo Sequencing and Homology Searching (2012) both
- Algorithms for the de novo sequencing of peptides from tandem mass spectra (2011) crossref
- Constrained De Novo Sequencing of Peptides with Application to Conotoxins (2011) crossref
- Resurrection of a clinical antibody: Template proteogenomic de novo proteomic sequencing and reverse engineering of an anti‐lymphotoxin‐α antibody (2011) both
- An antibody-based biomarker discovery method by mass spectrometry sequencing of complementarity determining regions (2011) both
- Algorithm Development of de novo Peptide Sequencing Via Tandem Mass Spectrometry (2010) crossref
- Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database (2010) both
- Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009) crossref