A Decoy-Free Approach to the Identification of Peptides

作者：Gonnelli Giulia; Stock Michiel; Verwaeren Jan; Maddelein Davy; De Baets Bernard; Martens Lennart^*; Degroeve Sven

来源：Journal of Proteome Research, 2015, 14(4): 1792-1798.

DOI：10.1021/pr501164r

• peptide identification
• decoy databases
• machine learning

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.

• 出版日期2015-4