title: A decoy-free approach to the identification of peptides.
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.
authors.affiliation: †Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Giulia
authors.initials: G
authors.lastname: Gonnelli
authors.affiliation: §Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
authors.forename: Michiel
authors.initials: M
authors.lastname: Stock
authors.affiliation: §Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Verwaeren
authors.affiliation: †Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Davy
authors.initials: D
authors.lastname: Maddelein
authors.affiliation: §Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
authors.forename: Bernard
authors.initials: B
authors.lastname: De Baets
authors.affiliation: †Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: †Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.|‡Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Sven
authors.initials: S
authors.lastname: Degroeve
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D016015:Logistic Models; D000069550:Machine Learning; D010455:Peptides / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D010455:Peptides
keywords: decoy databases; machine learning; peptide identification