pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data (Reprinted from vol 125, pg 89-97, 2015) | |
Chi, Hao1; He, Kun1; Yang, Bing2; Chen, Zhen3; Sun, Rui-Xiang1; Fan, Sheng-Bo1; Zhang, Kun1; Liu, Chao1; Yuan, Zuo-Fei1; Wang, Quan-Hui3 | |
刊名 | JOURNAL OF PROTEOMICS |
2015-11-03 | |
卷号 | 129页码:33-41 |
关键词 | Unrestricted database search Ion index In-depth interpretation High resolution MS/MS |
ISSN号 | 1874-3919 |
DOI | 10.1016/j.jprot.2015.07.019 |
英文摘要 | 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. This article is part of a Special Issue entitled: Computational Proteomics. (C) 2015 Elsevier Inc All rights reserved. |
WOS研究方向 | Biochemistry & Molecular Biology |
语种 | 英语 |
出版者 | ELSEVIER SCIENCE BV |
WOS记录号 | WOS:000364887600005 |
内容类型 | 期刊论文 |
源URL | [http://119.78.100.204/handle/2XEOYT63/9130] |
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 (Reprinted from vol 125, pg 89-97, 2015)[J]. JOURNAL OF PROTEOMICS,2015,129:33-41. |
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 (Reprinted from vol 125, pg 89-97, 2015).JOURNAL OF PROTEOMICS,129,33-41. |
MLA | Chi, Hao,et al."pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data (Reprinted from vol 125, pg 89-97, 2015)".JOURNAL OF PROTEOMICS 129(2015):33-41. |
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