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

	PFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry
	Wang, LH; Li, DQ; Fu, Y; Wang, HP; Zhang, JF; Yuan, ZF; Sun, RX; Zeng, R; He, SM; Gao, W
刊名	RAPID COMMUNICATIONS IN MASS SPECTROMETRY
	2007
卷号	21 期号:18 页码:2985-2991
通讯作者	He, SM (reprint author), Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China.,smhe@ict.ac.cn ; wgao@ict.ac.cn
英文摘要	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.
学科主题	Chemistry; Spectroscopy
类目[WOS]	Chemistry, Analytical ; Spectroscopy
关键词[WOS]	SPECTRAL DATA ; SEQUENCE DATABASES ; FRAGMENT IONS ; MS-MS ; PROTEOMICS ; MODEL
收录类别	SCI
语种	英语
WOS记录号	WOS:000249457800009
内容类型	期刊论文
版本	出版稿
源URL	[http://202.127.25.143/handle/331003/1628]
专题	上海生化细胞研究所_上海生科院生化细胞研究所
推荐引用方式 GB/T 7714	Wang, LH,Li, DQ,Fu, Y,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, LH.,Li, DQ.,Fu, Y.,Wang, HP.,Zhang, JF.,...&Gao, W.(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, LH,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.