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1.	Granholm, Viktor, 1986-, et al. (author) Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics 2013 In: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 80, s. 123-131 Journal article (peer-reviewed)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.

Granholm, Viktor, 1986-, et al. (author)
Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics
2013
In: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 80, s. 123-131
Journal article (peer-reviewed)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.

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