title: PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics.
abstract: In this study, we presented a quality control tool named PepDistiller to facilitate the validation of MASCOT search results. By including the number of tryptic termini, and integrating a refined false discovery rate (FDR) calculation method, we demonstrated the improved sensitivity of peptide identifications obtained from semitryptic search results. Based on the analysis of a complex data set, approximately 7% more peptide identifications were obtained using PepDistiller than using MASCOT Percolator. Moreover, the refined method generated lower FDR estimations than the percentage of incorrect target (PIT) fixed method applied in Percolator. Using a standard data set, we further demonstrated the increased accuracy of the refined FDR estimations relative to the PIT-fixed FDR estimations. PepDistiller is fast and convenient to use, and is freely available for academic access. The software can be downloaded from http://www.bprc.ac.cn/pepdistiller.
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Songfeng
authors.initials: S
authors.lastname: Wu
authors.forename: Chengpu
authors.initials: C
authors.lastname: Zhang
authors.forename: Cheng
authors.initials: C
authors.lastname: Chang
authors.forename: Jiyang
authors.initials: J
authors.lastname: Zhang
authors.forename: Jie
authors.initials: J
authors.lastname: Ma
authors.forename: Liwei
authors.initials: L
authors.lastname: Li
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Qian
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Fuchu
authors.initials: F
authors.lastname: He
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D010455:Peptides / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides