An efficient parallelization of phosphorylated peptide and protein identification
文献类型：期刊论文
| 作者 | Wang, Leheng1,2; Wang, Wenping1,2,3; Chi, Hao1,2,3; Wu, Yanjie1,2,3; Li, You1,2,3; Fu, Yan1,2; Zhou, Chen1,2,3; Sun, Ruixiang1,2; Wang, Haipeng1,2,3; Liu, Chao1,2,3 |
| 刊名 | Rapid communications in mass spectrometry
 |
| 出版日期 | 2010-06-01 |
| 卷号 | 24期号:12页码:1791-1798 |
| ISSN号 | 0951-4198 |
| DOI | 10.1002/rcm.4578 |
| 通讯作者 | He, si-min(smhe@ict.ac.cn) |
| 英文摘要 | 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. |
| WOS关键词 | TANDEM MASS-SPECTROMETRY ; LARGE-SCALE PROTEOMICS ; SEQUENCE DATABASES ; FRAGMENT IONS ; SPECTRA ; SEARCH ; SOFTWARE ; MS/MS ; PROTEOGENOMICS ; ANNOTATION |
| WOS研究方向 | Biochemistry & Molecular Biology ; Chemistry ; Spectroscopy |
| WOS类目 | Biochemical Research Methods ; Chemistry, Analytical ; Spectroscopy |
| 语种 | 英语 |
| WOS记录号 | WOS:000278661400010 |
| 出版者 | JOHN WILEY & SONS LTD |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2406611 |
| 专题 | 中国科学院大学 |
| 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. |
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来源：中国科学院大学
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