pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization

doi:10.1021/acs.jproteome.7b00428

	pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization
	Yang, Hao 1,2; Chi, Hao 1; Zhou, Wen-Jing 1,2; Zeng, Wen-Feng 1,2; Liu, Chao 1; Wang, Rui-Min 1,2; Wang, Zhao-Wei 1,2; Niu, Xiu-Nan 1,2; Chen, Zhen-Lin 1,2; He, Si-Min 1,2
	2018
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	17 期号:1 页码:119-128
摘要	MS-based de novo peptide sequencing has been improved remarkably with significant development of mass-spectrometry and computational approaches but still lacks quality-control methods. Here we proposed a novel algorithm pSite to evaluate the confidence of each amino acid rather than the full-length peptides obtained by de novo peptide sequencing. A semi supervised learning approach was used to discriminate correct amino acids from random one; then, an expectation-maximization algorithm was used to adaptively control the false amino-acid rate (FAR). On three test data sets, pSite recalled 86% more amino acids on average than PEAKS at the FAR of 5%. pSite also performed superiorly on the modification site localization problem, which is essentially a special case of amino acid confidence evaluation. On three phosphopeptide data sets, at the false localization rate of 1%, the average recall of pSite was 91% while those of Ascore and phosphoRS were 64 and 63%, respectively. pSite covered 98% of Ascore and phosphoRS results and contributed 21% more phosphorylation sites. Further analyses show that the use of distinct fragmentation features in high-resolution MS/MS spectra, such as neutral loss ions, played an important role in improving the precision of pSite. In summary, the effective and universal model together with the extensive use of spectral information makes pSite an excellent quality control tool for both de novo peptide sequencing and modification site localization.
关键词	tandem mass spectrometry de novo peptide sequencing modification site localization phosphorylation
DOI	10.1021/acs.jproteome.7b00428
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2016YFA0501301] ; National Natural Science Foundation of China[31470805] ; Youth Innovation Promotion Association CAS[2014091] ; National High Technology Research and Development Program of China (863)[2014AA020902] ; National High Technology Research and Development Program of China (863)[2014AA020901]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000419749800012
出版者	AMER CHEMICAL SOC
引用统计	被引频次：13[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/2XEOYT63/5571
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, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Yang, Hao,Chi, Hao,Zhou, Wen-Jing,et al. pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization[J]. JOURNAL OF PROTEOME RESEARCH,2018,17(1):119-128.
APA	Yang, Hao.,Chi, Hao.,Zhou, Wen-Jing.,Zeng, Wen-Feng.,Liu, Chao.,...&He, Si-Min.(2018).pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization.JOURNAL OF PROTEOME RESEARCH,17(1),119-128.
MLA	Yang, Hao,et al."pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization".JOURNAL OF PROTEOME RESEARCH 17.1(2018):119-128.