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Instance Based Algorithm for Posterior Probability Calculation by Target-Decoy Strategy to Improve Protein Identifications
Jiang, Xinning1,2; Dong, Xiaoli1,3; Ye, Mingliang1; Zou, Hanfa1; Zou HF(邹汉法); Zou HF(邹汉法)
刊名ANALYTICAL CHEMISTRY
2008-12-01
ISSN0003-2700
DOI10.1021/ac8017229
80期:23页:9326-9335
收录类别SCI
文章类型Article
部门归属18
项目归属1809
产权排名1;1
WOS标题词Science & Technology ; Physical Sciences
类目[WOS]Chemistry, Analytical
研究领域[WOS]Chemistry
关键词[WOS]TANDEM MASS-SPECTROMETRY ; INDUCED DISSOCIATION SPECTRA ; PEPTIDE MS/MS SPECTRA ; NEAREST-NEIGHBOR RULE ; DATABASE SEARCH ; STATISTICAL-MODEL ; SHOTGUN PROTEOMICS ; YEAST PROTEOME ; SEQUEST ; VALIDATION
英文摘要The target-decoy database search strategy is often applied to determine the global false-discovery rate (FDR) of peptide identifications in proteome research. However, the confidence of individual peptide identification is typically not determined. In this study, we introduced an approach for the calculation of posterior probability of individual peptide identification from the "local false-discovery rate" (local FDR), which is also determined based on a target-decoy database search. The peptide identification scores output by the database search algorithm were weighted by their discriminating power using a Shannon information entropy based strategy. Then the local FDR of a peptide identification was calculated based on the fraction of decoy identifications among its nearest neighbors within a small space defined by these weighted scores. It was demonstrated that the calculated probability matched the actual probability precisely, and it provided powerful discriminating performance between true positive and false positive identifications. Hence, the sensitivity for peptide identification as well as protein identification was significantly improved when the calculated probability was used to process different proteome data sets. As an instance based strategy, this algorithm provides a safe way for the posterior probability calculation and should work well for datasets with different characteristics.
语种英语
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WOS记录号WOS:000261335600061
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被引频次:3[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/100923
专题中国科学院大连化学物理研究所
通讯作者Zou HF(邹汉法); Zou HF(邹汉法)
作者单位1.Chinese Acad Sci, Dalian Inst Chem Phys, Natl Chromatog R&A Ctr, Dalian 116023, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
3.Zhejiang Univ, Dept Chem, Hangzhou 310028, Peoples R China
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Jiang, Xinning,Dong, Xiaoli,Ye, Mingliang,et al. Instance Based Algorithm for Posterior Probability Calculation by Target-Decoy Strategy to Improve Protein Identifications[J]. ANALYTICAL CHEMISTRY,2008,80(23):9326-9335.
APA Jiang, Xinning,Dong, Xiaoli,Ye, Mingliang,Zou, Hanfa,邹汉法,&邹汉法.(2008).Instance Based Algorithm for Posterior Probability Calculation by Target-Decoy Strategy to Improve Protein Identifications.ANALYTICAL CHEMISTRY,80(23),9326-9335.
MLA Jiang, Xinning,et al."Instance Based Algorithm for Posterior Probability Calculation by Target-Decoy Strategy to Improve Protein Identifications".ANALYTICAL CHEMISTRY 80.23(2008):9326-9335.
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