pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics

doi:10.1021/acs.jproteome.8b00993

	pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics
	Zhou, Wen-Jing 1,2; Yang, Hao 1,2; Zeng, Wen-Feng 1,2; Zhang, Kun 1,2; Chi, Hao 1,2; He, Si-Min 1,2
	2019-07-01
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	18 期号:7 页码:2747-2758
摘要	As the de facto validation method in mass spectrometry-based proteomics, the target-decoy approach determines a threshold to estimate the false discovery rate and then filters those identifications beyond the threshold. However, the incorrect identifications within the threshold are still unknown and further validation methods are needed. In this study, we characterized a framework of validation and investigated a number of common and novel validation methods. We first defined the accuracy of a validation method by its false-positive rate (FPR) and false-negative rate (FNR) and, further, proved that a validation method with lower FPR and FNR led to identifications with higher sensitivity and precision. Then we proposed a validation method named pValid that incorporated an open database search and a theoretical spectrum prediction strategy via a machine-learning technology. pValid was compared with four common validation methods as well as a synthetic peptide validation method. Tests on three benchmark data sets indicated that pValid had an FPR of 0.03% and an FNR of 1.79% on average, both superior to the other four common validation methods. Tests on a synthetic peptide data set also indicated that the FPR and FNR of pValid were better than those of the synthetic peptide validation method. Tests on a large-scale human proteome data set indicated that pValid successfully flagged the highest number of incorrect identifications among all five methods. Further considering its cost-effectiveness, pValid has the potential to be a feasible validation tool for peptide identification.
关键词	tandem mass spectrometry target-decoy approach validation methods false-positive rate false-negative rate
DOI	10.1021/acs.jproteome.8b00993
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2016YFA0501300] ; CAS Interdisciplinary Innovation Team[Y604061000] ; National Natural Science Foundation of China[21475141] ; Youth Innovation Promotion Association CAS[2014091]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000474795500006
出版者	AMER CHEMICAL SOC
引用统计	被引频次：15[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4320
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chi, Hao; He, Si-Min
作者单位	1.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Inst Comp Technol, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Zhou, Wen-Jing,Yang, Hao,Zeng, Wen-Feng,et al. pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics[J]. JOURNAL OF PROTEOME RESEARCH,2019,18(7):2747-2758.
APA	Zhou, Wen-Jing,Yang, Hao,Zeng, Wen-Feng,Zhang, Kun,Chi, Hao,&He, Si-Min.(2019).pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics.JOURNAL OF PROTEOME RESEARCH,18(7),2747-2758.
MLA	Zhou, Wen-Jing,et al."pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics".JOURNAL OF PROTEOME RESEARCH 18.7(2019):2747-2758.