Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics
2013 (English)In: Journal of Proteomics, ISSN 1874-3919, Vol. 80, 123-131 p.Article in journal (Refereed) Published
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.
Shotgun proteomics, Peptides, Statistics
Bioinformatics (Computational Biology)
Research subject Biochemistry towards Bioinformatics
IdentifiersURN: urn:nbn:se:su:diva-89873DOI: 10.1016/j.jprot.2012.12.007ISI: 000317544700010OAI: oai:DiVA.org:su-89873DiVA: diva2:621263