期刊
JOURNAL OF PROTEOMICS
卷 80, 期 -, 页码 123-131出版社
ELSEVIER
DOI: 10.1016/j.jprot.2012.12.007
关键词
Shotgun proteomics; Peptides; Statistics
资金
- Swedish Research Council
- Science for Life Laboratory
- Lawski Foundation
- NIH [P41 467 GM103533, R01 GM096306]
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. (C) 2013 Elsevier B.V. All rights reserved.
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