A Decoy-Free Approach to the Identification of Peptides
Journal of Proteome Research2015Vol. 14(4), pp. 1792–1798
Citations Over TimeTop 11% of 2015 papers
Giulia Gonnelli, Michiel Stock, Jan Verwaeren, Davy Maddelein, Bernard De Baets, Lennart Martens, Sven Degroeve
Abstract
A growing number of proteogenomics and metaproteomics studies indicate potential limitations of the application of the "decoy" database paradigm used to separate correct peptide identifications from incorrect ones in traditional shotgun proteomics. We therefore propose a binary classifier called Nokoi that allows fast yet reliable decoy-free separation of correct from incorrect peptide-to-spectrum matches (PSMs). Nokoi was trained on a very large collection of heterogeneous data using ranks supplied by the Mascot search engine to label correct and incorrect PSMs. We show that Nokoi outperforms Mascot and achieves a performance very close to that of Percolator at substantially higher processing speeds.
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