title: PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification.
abstract: Many software tools have been developed for the automated identification of peptides from tandem mass spectra. The accuracy and sensitivity of the identification software via database search are critical for successful proteomics experiments. A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search. PEAKS DB achieves significantly improved accuracy and sensitivity over two other commonly used software packages. Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of overconfidence that exists in the conventional target decoy method for certain types of peptide identification software.
authors.affiliation: Bioinformatics Solutions Inc., Waterloo, Ontario N2L 6J2, Canada.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Lei
authors.initials: L
authors.lastname: Xin
authors.forename: Baozhen
authors.initials: B
authors.lastname: Shan
authors.forename: Weiwu
authors.initials: W
authors.lastname: Chen
authors.forename: Mingjie
authors.initials: M
authors.lastname: Xie
authors.forename: Denis
authors.initials: D
authors.lastname: Yuen
authors.forename: Weiming
authors.initials: W
authors.lastname: Zhang
authors.forename: Zefeng
authors.initials: Z
authors.lastname: Zhang
authors.forename: Gilles A
authors.initials: GA
authors.lastname: Lajoie
authors.forename: Bin
authors.initials: B
authors.lastname: Ma
mesh_terms: D030562:Databases, Protein; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D020539:Sequence Analysis, Protein; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides