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Rapid and accurate peptide identification from tandem mass spectra
KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0001-5689-9797
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2008 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 7, no 7, 3022-3027 p.Article in journal (Refereed) Published
Abstract [en]

Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification. Crux is implemented in C and is distributed with source code freely to noncommercial users.

Place, publisher, year, edition, pages
2008. Vol. 7, no 7, 3022-3027 p.
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-48852DOI: 10.1021/pr800127yISI: 000257449500041PubMedID: 18505281OAI: oai:DiVA.org:kth-48852DiVA: diva2:458747
Note
QC 20111128Available from: 2011-11-23 Created: 2011-11-23 Last updated: 2017-12-08Bibliographically approved

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Käll, Lukas

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