Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing

	Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing
	Li, Y; Chi, H; Wang, LH; Wang, HP; Fu, Y; Yuan, ZF; Li, SJ; Liu, YS; Sun, RX; Zeng, R
刊名	RAPID COMMUNICATIONS IN MASS SPECTROMETRY
	2010
卷号	24 期号:6 页码:807-814
通讯作者	He, SM (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China.,smhe@jdl.ac.cn
英文摘要	Database searching is the technique of choice for shotgun proteomics, and to date much research effort has been spent on improving its effectiveness. However, database searching faces a serious challenge of efficiency, considering the large numbers of mass spectra and the ever fast increase in peptide databases resulting from genome translations, enzymatic digestions, and post-translational modifications. In this study, we conducted systematic research on speeding up database search engines for protein identification and illustrate the key points with the specific design of the pFind 2.1 search engine as a running example. Firstly, by constructing peptide indexes, pFind achieves a speedup of two to three compared with that without peptide indexes. Secondly, by constructing indexes for observed precursor and fragment ions, pFind achieves another speedup of two. As a result, pFind compares very favorably with predominant search engines such as Mascot, SEQUEST and X!Tandem. Copyright (C) 2010 John Wiley & Sons, Ltd.
学科主题	Chemistry; Spectroscopy
类目[WOS]	Chemistry, Analytical ; Spectroscopy
关键词[WOS]	SEQUENCE DATABASES ; IDENTIFICATION ; ALGORITHM ; PHOSPHORYLATION ; PROTEINS
收录类别	SCI
语种	英语
WOS记录号	WOS:000276111100014
内容类型	期刊论文
版本	出版稿
源URL	[http://202.127.25.143/handle/331003/1022]
专题	上海生化细胞研究所_上海生科院生化细胞研究所
推荐引用方式 GB/T 7714	Li, Y,Chi, H,Wang, LH,et al. Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing[J]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY,2010,24(6):807-814.
APA	Li, Y.,Chi, H.,Wang, LH.,Wang, HP.,Fu, Y.,...&He, SM.(2010).Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing.RAPID COMMUNICATIONS IN MASS SPECTROMETRY,24(6),807-814.
MLA	Li, Y,et al."Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing".RAPID COMMUNICATIONS IN MASS SPECTROMETRY 24.6(2010):807-814.