ArticleMolecular & cellular proteomics : MCP2011
Gapped spectral dictionaries and their applications for database searches of tandem mass spectra.
Article in Molecular & cellular proteomics : MCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 23 citations in OpenAlex.
- A graph-based filtering method for top-down mass spectral identification.BMC genomics · 2018Article
- Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry.Proteomics · 2018Article
- A Spectrum Graph-Based Protein Sequence Filtering Algorithm for Proteoform Identification by Top-Down Mass Spectrometry.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2017Article
- PGx: Putting Peptides to BED.Journal of proteome research · 2016Article
- MS-GF+ makes progress towards a universal database search tool for proteomics.Nature communications · 2014Article
- UniNovo: a universal tool for de novo peptide sequencing.Bioinformatics (Oxford, England) · 2013Article
- Current algorithmic solutions for peptide-based proteomics data generation and identification.Current opinion in biotechnology · 2013Review
- Spectrum Identification using a Dynamic Bayesian Network Model of Tandem Mass Spectra.Uncertainty in artificial intelligence : proceedings of the ... conference. Conference on Uncertainty in Artificial Intelligence · 2012Article
- Speeding up tandem mass spectral identification using indexes.Bioinformatics (Oxford, England) · 2012Article
- De novo sequencing and homology searching.Molecular & cellular proteomics : MCP · 2012Article
- Computational mass spectrometry-based proteomics.PLoS computational biology · 2011Article
- The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search.Molecular & cellular proteomics : MCP · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the limitation of the Spectral Dictionary approach. We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS searches. Our MS-Gapped-Dictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications (such as searches in the six-frame translation of the human genome) that are prohibitively time consuming with existing approaches. MS-Gapped-Dictionary generates gapped peptides that occupy a niche between accurate but short peptide sequence tags and long but inaccurate full length peptide reconstructions. We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches.
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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.