Shotgun Protein Sequencing with Meta-contig Assembly
peer-reviewed · Molecular & Cellular Proteomics · 2012
| Date | 2012-10-01 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | algorithm |
| DOI | 10.1074/mcp.M111.015768 |
| Citations (OpenAlex) | 29 |
| Venue 2-year citedness | 4.69 |
Abstract
Full-length de novo sequencing from tandem mass (MS/MS) spectra of unknown proteins such as antibodies or proteins from organisms with unsequenced genomes remains a challenging open problem. Conventional algorithms designed to individually sequence each MS/MS spectrum are limited by incomplete peptide fragmentation or low signal to noise ratios and tend to result in short de novo sequences at low sequencing accuracy. Our shotgun protein sequencing (SPS) approach was developed to ameliorate these limitations by first finding groups of unidentified spectra from the same peptides (contigs) and then deriving a consensus de novo sequence for each assembled set of spectra (contig sequences). But whereas SPS enables much more accurate reconstruction of de novo sequences longer than can be recovered from individual MS/MS spectra, it still requires error-tolerant matching to homologous proteins to group smaller contig sequences into full-length protein sequences, thus limiting its effectiveness on sequences from poorly annotated proteins. Using low and high resolution CID and high resolution HCD MS/MS spectra, we address this limitation with a Meta-SPS algorithm designed to overlap and further assemble SPS contigs into Meta-SPS de novo contig sequences extending as long as 100 amino acids at over 97% accuracy without requiring any knowledge of homologous protein sequences. We demonstrate Meta-SPS using distinct MS/MS data sets obtained with separate enzymatic digestions and discuss how the remaining de novo sequencing limitations relate to MS/MS acquisition settings.
Methods and tools
- Meta-SPS: Shotgun protein sequencing with meta-contig assembly for longer de novo protein contigs.
Cites (17)
- pNovo: De novo Peptide Sequencing and Identification Using HCD Spectra (2010) both
- Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy (2009) both
- Automated de novo protein sequencing of monoclonal antibodies (2008) both
- De Novo Sequencing of Unique Sequence Tags for Discovery of Post-Translational Modifications of Proteins (2008) both
- Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins (2007) both
- Protein identification by spectral networks analysis (2007) both
- De Novo Peptide Sequencing and Identification with Precision Mass Spectrometry (2007) both
- InsPecT: Identification of Posttranslationally Modified Peptides from Tandem Mass Spectra (2005) both
- SPIDER: software for protein identification from sequence tags with de novo sequencing error (2005) crossref
- Identification of Protein Modifications Using MS/MS de Novo Sequencing and the OpenSea Alignment Algorithm (2005) both
- PepNovo: de novo peptide sequencing via probabilistic network modeling (2005) both
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004) both
- PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003) crossref
- Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching (2001) both
- De novo peptide sequencing via tandem mass spectrometry (1999) both
- Sequence database searches via de novo peptide sequencing by tandem mass spectrometry (1997) both
- Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags (1994) both
Cited by (17)
- Reference-free protein sequencing by consensus assembly of redundant de novo peptide reads (2026) both
- Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions (2025) crossref
- A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics (2024) 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
- Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies (2022) both
- Highly Robust de Novo Full-Length Protein Sequencing (2021) crossref
- A potential golden age to come—current tools, recent use cases, and future avenues for de novo sequencing in proteomics (2018) crossref
- Antibody de novo Sequencing (2017) crossref
- A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom (2017) both
- Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination (2017) both
- De Novo MS/MS Sequencing of Native Human Antibodies (2017) both
- Complete De Novo Assembly of Monoclonal Antibody Sequences (2016) both
- PepExplorer: A Similarity-driven Tool for Analyzing de Novo Sequencing Results (2014) both
- De Novo Protein Sequencing by Combining Top-Down and Bottom-Up Tandem Mass Spectra (2014) crossref
- Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013) both
- Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013) both