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P ep D istiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics
Author(s) -
Li Ning,
Wu Songfeng,
Zhang Chengpu,
Chang Cheng,
Zhang Jiyang,
Ma Jie,
Li Liwei,
Qian Xiaohong,
Xu Ping,
Zhu Yunping,
He Fuchu
Publication year - 2012
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100167
Subject(s) - shotgun proteomics , proteomics , peptide , sensitivity (control systems) , shotgun , chemistry , quality (philosophy) , computational biology , chromatography , biology , biochemistry , engineering , physics , quantum mechanics , electronic engineering , gene
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.