ArticleMolecular & cellular proteomics : MCP2012
Shotgun protein sequencing with meta-contig assembly.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- A Handle on Mass Coincidence Errors inJournal of proteome research · 2024Article
- Global detection of human variants and isoforms by deep proteome sequencing.Nature biotechnology · 2023Article
- Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly.Briefings in bioinformatics · 2023Article
- Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation.Analytical chemistry · 2020Article
- A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom.Scientific data · 2017Article
- Database-independent Protein Sequencing (DiPS) Enables Full-lengthMolecular & cellular proteomics : MCP · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- De Novo MS/MS Sequencing of Native Human Antibodies.Journal of proteome research · 2017Article
- Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks.Molecular & cellular proteomics : MCP · 2016Article
- Complete De Novo Assembly of Monoclonal Antibody Sequences.Scientific reports · 2016Article
- The generating function approach for Peptide identification in spectral networks.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Making proteomics data accessible and reusable: current state of proteomics databases and repositories.Proteomics · 2015Review
- PepExplorer: a similarity-driven tool for analyzing de novo sequencing results.Molecular & cellular proteomics : MCP · 2014Article
- Neutron-encoded signatures enable product ion annotation from tandem mass spectra.Molecular & cellular proteomics : MCP · 2013Article
- Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides.Journal of proteome research · 2013Article
- The spectral networks paradigm in high throughput mass spectrometry.Molecular bioSystems · 2012Review
- Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.