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	Open ms/ms spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
	Ye, Ding1,2,3; Fu, Yan1,2; Sun, Rui-Xiang1,2; Wang, Hai-Peng1,2,3; Yuan, Zuo-Fei1,2,3; Chi, Hao1,2,3; He, Si-Min1,2
刊名	Bioinformatics
	2010-06-15
卷号	26期号:12页码:I399-i406
ISSN号	1367-4803
DOI	10.1093/bioinformatics/btq185
通讯作者	Fu, yan(yfu@ict.ac.cn)
英文摘要	Motivation: identification of post-translationally modified proteins has become one of the central issues of current proteomics. spectral library search is a new and promising computational approach to mass spectrometry-based protein identification. however, its potential in identification of unanticipated post-translational modifications has rarely been explored. the existing spectral library search tools are designed to match the query spectrum to the reference library spectra with the same peptide mass. thus, spectra of peptides with unanticipated modifications cannot be identified. results: in this article, we present an open spectral library search tool, named pmatch. it extends the existing library search algorithms in at least three aspects to support the identification of unanticipated modifications. first, the spectra in library are optimized with the full peptide sequence information to better tolerate the peptide fragmentation pattern variations caused by some modification(s). second, a new scoring system is devised, which uses charge-dependent mass shifts for peak matching and combines a probability-based model with the general spectral dot-product for scoring. third, a target-decoy strategy is used for false discovery rate control. to demonstrate the effectiveness of pmatch, a library search experiment was conducted on a public dataset with over 40 000 spectra in comparison with spectrast, the most popular library search engine. additional validations were done on four published datasets including over 150 000 spectra. the results showed that pmatch can effectively identify unanticipated modifications and significantly increase spectral identification rate. availability: http://pfind.ict.ac.cn/pmatch/ contact: yfu@ict.ac.cn; rxsun@ict.ac.cn supplementary information: supplementary data are available at bioinformatics online.
WOS关键词	TANDEM MASS-SPECTROMETRY ; PEPTIDE IDENTIFICATION ; PROTEIN IDENTIFICATION ; PROTEOMICS ; DATABASE ; SOFTWARE ; ACCURACY ; OPTIMIZATION ; SITES ; PFIND
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000278689000049
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2410669
专题	中国科学院大学
通讯作者	Fu, Yan
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Ye, Ding,Fu, Yan,Sun, Rui-Xiang,et al. Open ms/ms spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate[J]. Bioinformatics,2010,26(12):I399-i406.
APA	Ye, Ding.,Fu, Yan.,Sun, Rui-Xiang.,Wang, Hai-Peng.,Yuan, Zuo-Fei.,...&He, Si-Min.(2010).Open ms/ms spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate.Bioinformatics,26(12),I399-i406.
MLA	Ye, Ding,et al."Open ms/ms spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate".Bioinformatics 26.12(2010):I399-i406.

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