pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

doi:10.1016/j.jprot.2015.05.009

	pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data
	Chi, Hao 1; He, Kun 1; Yang, Bing 2; Chen, Zhen 3; Sun, Rui-Xiang 1; Fan, Sheng-Bo 1; Zhang, Kun 1; Liu, Chao 1; Yuan, Zuo-Fei 1; Wang, Quan-Hui 3; Liu, Si-Qi 3; Dong, Meng-Qiu 2; He, Si-Min 1
	2015-07-01
发表期刊	JOURNAL OF PROTEOMICS
ISSN	1874-3919
卷号	125 页码:89-97
摘要	Database search is the dominant approach in high-throughput proteomic analysis. However, the interpretation rate of MS/MS spectra is very low in such a restricted mode, which is mainly due to unexpected modifications and irregular digestion types. In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi- and non-specific digestions, as well as those with unexpected modifications or mutations, can be effectively identified using Alioth and confidently validated using other search engines. The average processing speed of Alioth is 5-10 times faster than some other unrestricted search engines and is comparable to or even faster than the restricted search algorithms tested. (C) 2015 Elsevier B.V. All rights reserved.
关键词	Unrestricted database search Ion index In-depth interpretation High resolution MS/MS
DOI	10.1016/j.jprot.2015.05.009
收录类别	SCI
语种	英语
资助项目	National Key Basic Research and Development Program of China (973)[2013CB911203] ; National Key Basic Research and Development Program of China (973)[2012CB910602] ; National Key Basic Research and Development Program of China (973)[2010CB912701] ; National High Technology Research and Development Program of China (863)[2014AA020902] ; National High Technology Research and Development Program of China (863)[2014AA020901] ; CAS Knowledge Innovation Program[KGCX1-YW-13] ; CAS Knowledge Innovation Program[ICT-20126033]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000357243000008
出版者	ELSEVIER SCIENCE BV
引用统计	被引频次：46[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/2XEOYT63/9628
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.Natl Inst Biol Sci, Beijing 102206, Peoples R China 3.Chinese Acad Sci, Beijing Inst Genom, Beijing 100029, Peoples R China
推荐引用方式 GB/T 7714	Chi, Hao,He, Kun,Yang, Bing,et al. pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data[J]. JOURNAL OF PROTEOMICS,2015,125:89-97.
APA	Chi, Hao.,He, Kun.,Yang, Bing.,Chen, Zhen.,Sun, Rui-Xiang.,...&He, Si-Min.(2015).pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data.JOURNAL OF PROTEOMICS,125,89-97.
MLA	Chi, Hao,et al."pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data".JOURNAL OF PROTEOMICS 125(2015):89-97.