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Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics
KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-4035-5258
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, E-ISSN 1876-7737, 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
Identifiers
URN: urn:nbn:se:kth:diva-122116DOI: 10.1016/j.jprot.2012.12.007ISI: 000317544700010Scopus ID: 2-s2.0-84873695876OAI: oai:DiVA.org:kth-122116DiVA: diva2:621262
Funder
Swedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20130514

Available from: 2013-05-14 Created: 2013-05-13 Last updated: 2017-12-06Bibliographically approved

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Käll, Lukas

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
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Output format
  • html
  • text
  • asciidoc
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