title: High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics.
abstract: In a previous paper we introduced a novel model-based approach (OLAV) to the problem of identifying peptides via tandem mass spectrometry, for which early implementations showed promising performance. We recently further improved this performance to a remarkable level (1-2% false positive rate at 95% true positive rate) and characterized key properties of OLAV like robustness and training set size. We present these results in a synthetic and coherent way along with detailed performance comparisons, a new scoring component making use of peptide amino acidic composition, and new developments like automatic parameter learning. Finally, we discuss the impact of OLAV on the automation of proteomics projects.
authors.affiliation: GeneProt Inc., Rue Pré de la Fontaine 2, Case Postale 125, 1217 Meyrin, Switzerland. jacques.collinge@geneprot.com
authors.forename: Jacques
authors.initials: J
authors.lastname: Colinge
authors.forename: Alexandre
authors.initials: A
authors.lastname: Masselot
authors.forename: Isabelle
authors.initials: I
authors.lastname: Cusin
authors.forename: Eve
authors.initials: E
authors.lastname: Mahé
authors.forename: Anne
authors.initials: A
authors.lastname: Niknejad
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Argoud-Puy
authors.forename: Samia
authors.initials: S
authors.lastname: Reffas
authors.forename: Nassima
authors.initials: N
authors.lastname: Bederr
authors.forename: Anne
authors.initials: A
authors.lastname: Gleizes
authors.forename: Pierre-Antoine
authors.initials: PA
authors.lastname: Rey
authors.forename: Lydie
authors.initials: L
authors.lastname: Bougueleret
mesh_terms: D000465:Algorithms; D001331:Automation; D005189:False Positive Reactions; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012372:ROC Curve; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods; D013997:Time Factors
chemical_list: D010455:Peptides