title: pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry.
abstract: 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/.
authors: Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, P.R. China.
authors: Le-Heng
authors: LH
authors: Wang
authors: De-Quan
authors: DQ
authors: Li
authors: Yan
authors: Y
authors: Fu
authors: Hai-Peng
authors: HP
authors: Wang
authors: Jing-Fen
authors: JF
authors: Zhang
authors: Zuo-Fei
authors: ZF
authors: Yuan
authors: Rui-Xiang
authors: RX
authors: Sun
authors: Rong
authors: R
authors: Zeng
authors: Si-Min
authors: SM
authors: He
authors: Wen
authors: W
authors: Gao
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D012986:Software Validation; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins