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Fast and accurate database searches with MS-GF+percolator
KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2014 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, no 2, 890-897 p.Article in journal (Refereed) Published
Abstract [en]

One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.

Place, publisher, year, edition, pages
2014. Vol. 13, no 2, 890-897 p.
Keyword [en]
bioinformatics, confidence estimation, machine learning, shotgun proteomics
National Category
Other Chemistry Topics Biochemistry and Molecular Biology
URN: urn:nbn:se:kth:diva-142798DOI: 10.1021/pr400937nISI: 000331164100049ScopusID: 2-s2.0-84893830089OAI: diva2:704703
Swedish Foundation for Strategic Research Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceSwedish e‐Science Research CenterSwedish Research Council

QC 20140313

Available from: 2014-03-13 Created: 2014-03-12 Last updated: 2014-03-24Bibliographically approved

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Fernandez Navarro, JoséKäll, Lukas
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Science for Life Laboratory, SciLifeLabGene TechnologySeRC - Swedish e-Science Research Centre
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