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• W1965709178 abstract "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." @default.
• W1965709178 created "2016-06-24" @default.
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• W1965709178 date "2013-03-01" @default.
• W1965709178 modified "2023-10-13" @default.
• W1965709178 title "Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics" @default.
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• W1965709178 doi "https://doi.org/10.1016/j.jprot.2012.12.007" @default.
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