PFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry

doi:10.1002/rcm.3173

	PFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry
	Wang, Le-heng ; Li, De-Quan ; Fu, Yan ; Wang, Hai-Peng ; Zhang, Jing-Fen ; Yuan, Zuo-Fei ; Sun, Rui-Xiang ; Zeng, Rong ; He, Si-Min ; Gao, Wen
	2007
发表期刊	RAPID COMMUNICATIONS IN MASS SPECTROMETRY
ISSN	0951-4198
卷号	21 期号:18 页码:2985-2991
摘要	This paper describes the pFind 2.0 software package for peptide and protein identification via tandem mass spectrometry. Firstly, the most important feature of pFind 2.0 is that it offers a modularized and customized platform for third parties to test and compare their algorithms. The developers can create their own modules following the open application programming interface (API) standards and then add it into workflows in place of the default modules. In addition, to accommodate different requirements, the package provides four automated workflows adopting different algorithm modules, executing processes and result reports. Based on this design, pFind 2.0 provides an automated target-decoy database search strategy: The user can just specify a certain false positive rate (FPR) and start searching. Then the system will return the protein identification results automatically filtered by such an estimated FPR. Secondly, pFind 2.0 is also of high accuracy and high speed. Many pragmatic preprocessing, peptide-scoring, validation, and protein inference algorithms have been incorporated. To speed up the searching process, a toolbox for indexing protein databases is developed for high-throughput applications and all modules are implemented under a new architecture designed for large-scale parallel and distributed searching. An experiment on a public dataset shows that pFind 2.0 can identify more peptides than SEQUEST and Mascot at the 1% FPR. It is also demonstrated that this version of pFind 2.0 has better usability and higher speed than its previous versions. The software and more detailed supplementary information can both be accessed at http://pfind.ict.ac.cn/. Copyright (c) 2007 John Wiley & Sons, Ltd.
DOI	10.1002/rcm.3173
收录类别	SCI
语种	英语
WOS研究方向	Chemistry ; Spectroscopy
WOS类目	Chemistry, Analytical ; Spectroscopy
WOS记录号	WOS:000249457800009
出版者	JOHN WILEY & SONS LTD
引用统计	被引频次：178[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/2XEOYT63/10955
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, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Key Lab Proteom, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Key Lab Intelligent Informat Proc, Beijing 100080, Peoples R China 4.Grad Univ, Chinese Acad Sci, Beijing 100039, Peoples R China
推荐引用方式 GB/T 7714	Wang, Le-heng,Li, De-Quan,Fu, Yan,et al. PFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry[J]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY,2007,21(18):2985-2991.
APA	Wang, Le-heng.,Li, De-Quan.,Fu, Yan.,Wang, Hai-Peng.,Zhang, Jing-Fen.,...&Gao, Wen.(2007).PFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry.RAPID COMMUNICATIONS IN MASS SPECTROMETRY,21(18),2985-2991.
MLA	Wang, Le-heng,et al."PFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry".RAPID COMMUNICATIONS IN MASS SPECTROMETRY 21.18(2007):2985-2991.