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Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics
KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-5689-9797
2013 (English)In: Journal of Proteomics, ISSN 1874-3919, Vol. 80, 123-131 p.Article in journal (Refereed) Published
Abstract [en]

The analysis of a shotgun proteomics experiment results in a list of peptide-spectrum matches (PSMs) in which each fragmentation spectrum has been matched to a peptide in a database. Subsequently, most protein inference algorithms rank peptides according to the best-scoring PSM for each peptide. However, there is disagreement in the scientific literature on the best method to assess the statistical significance of the resulting peptide identifications. Here, we use a previously described calibration protocol to evaluate the accuracy of three different peptide-level statistical confidence estimation procedures: the classical Fisher's method, and two complementary procedures that estimate significance, respectively, before and after selecting the top-scoring PSM for each spectrum. Our experiments show that the latter method, which is employed by MaxQuant and Percolator, produces the most accurate, well-calibrated results.

Place, publisher, year, edition, pages
2013. Vol. 80, 123-131 p.
Keyword [en]
Shotgun proteomics, Peptides, Statistics
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:kth:diva-122116DOI: 10.1016/j.jprot.2012.12.007ISI: 000317544700010ScopusID: 2-s2.0-84873695876OAI: diva2:621262
Swedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience

QC 20130514

Available from: 2013-05-14 Created: 2013-05-13 Last updated: 2013-05-14Bibliographically approved

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Fernandez Navarro, JoséKäll, Lukas
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