An efficient parallelization of phosphorylated peptide and protein identification

doi:10.1002/rcm.4578

	An efficient parallelization of phosphorylated peptide and protein identification
	Wang, Leheng 1,2; Wang, Wenping 1,2,3; Chi, Hao 1,2,3; Wu, Yanjie 1,2,3; Li, You 1,2,3; Fu, Yan 1,2; Zhou, Chen 1,2,3; Sun, Ruixiang 1,2; Wang, Haipeng 1,2,3; Liu, Chao 1,2,3; Yuan, Zuofei 1,2,3; Xiu, Liyun 1,2,3; He, Si-Min 1,2
	2010-06-01
发表期刊	RAPID COMMUNICATIONS IN MASS SPECTROMETRY
ISSN	0951-4198
卷号	24 期号:12 页码:1791-1798
摘要	Protein sequence database search based on tandem mass spectrometry is an essential method for protein identification. As the computational demand increases, parallel computing has become an important technique for accelerating proteomics data analysis. In this paper, we discuss several factors which could affect the runtime of the pFind search engine and build an estimation model. Based on this model, effective on-line and off-line scheduling methods were developed. An experiment on the public dataset from PhosphoPep consisting of 100 RAW files of phosphopeptides shows that the speedup on 100 processors is 83.7. The parallel version can complete the identification task within 9 min, while a stand-alone process on a single PC takes more than 10 h. On another larger dataset consisting of 1 366 471 spectra, the speedup on 320 processors is 258.9 and the efficiency is 80.9%. Our approach can be applied to other similar search engines. Copyright (C) 2010 John Wiley & Sons, Ltd.
DOI	10.1002/rcm.4578
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] ; National Key Basic Research & Development Program (973) of China[2010CB912701] ; CAS[KGGX1-YW-13]
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry ; Spectroscopy
WOS类目	Biochemical Research Methods ; Chemistry, Analytical ; Spectroscopy
WOS记录号	WOS:000278661400010
出版者	JOHN WILEY & SONS LTD
引用统计	被引频次：9[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/2XEOYT63/12070
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, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, 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	Wang, Leheng,Wang, Wenping,Chi, Hao,et al. An efficient parallelization of phosphorylated peptide and protein identification[J]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY,2010,24(12):1791-1798.
APA	Wang, Leheng.,Wang, Wenping.,Chi, Hao.,Wu, Yanjie.,Li, You.,...&He, Si-Min.(2010).An efficient parallelization of phosphorylated peptide and protein identification.RAPID COMMUNICATIONS IN MASS SPECTROMETRY,24(12),1791-1798.
MLA	Wang, Leheng,et al."An efficient parallelization of phosphorylated peptide and protein identification".RAPID COMMUNICATIONS IN MASS SPECTROMETRY 24.12(2010):1791-1798.