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

doi:10.1002/rcm.4448

	Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing
	Li, You 1,2; Chi, Hao 1,2; Wang, Le-Heng 1; Wang, Hai-Peng 1,2; Fu, Yan 1; Yuan, Zuo-Fei 1,2; Li, Su-Jun 3; Liu, Yan-Sheng 3; Sun, Rui-Xiang 1; Zeng, Rong 3; He, Si-Min 1
	2010-03-01
发表期刊	RAPID COMMUNICATIONS IN MASS SPECTROMETRY
ISSN	0951-4198
卷号	24 期号:6 页码:807-814
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.
DOI	10.1002/rcm.4448
收录类别	SCI
语种	英语
资助项目	National High Technology Research and Development Program (863) of China[2007AA02Z315] ; National High Technology Research and Development Program (863) of China[2008AA02Z309] ; National Key Basic Research & Development Program (973) of China[2002CB713807] ; CAS Knowledge Innovation Program[KGGX1-YW-13]
WOS研究方向	Chemistry ; Spectroscopy
WOS类目	Chemistry, Analytical ; Spectroscopy
WOS记录号	WOS:000276111100014
出版者	JOHN WILEY & SONS LTD
引用统计	被引频次：30[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/2XEOYT63/12308
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	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.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Res Ctr Proteome Anal,Key Lab Prote, Shanghai 200031, Peoples R China
推荐引用方式 GB/T 7714	Li, You,Chi, Hao,Wang, Le-Heng,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, You.,Chi, Hao.,Wang, Le-Heng.,Wang, Hai-Peng.,Fu, Yan.,...&He, Si-Min.(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, You,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.