title: An efficient parallelization of phosphorylated peptide and protein identification.
abstract: 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.
authors.affiliation: Key Lab of Intelligent Information Processing, Chinese Academy of Sciences, Beijing 100190, P.R. China.
authors.forename: Leheng
authors.initials: L
authors.lastname: Wang
authors.forename: Wenping
authors.initials: W
authors.lastname: Wang
authors.forename: Hao
authors.initials: H
authors.lastname: Chi
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Wu
authors.forename: You
authors.initials: Y
authors.lastname: Li
authors.forename: Yan
authors.initials: Y
authors.lastname: Fu
authors.forename: Chen
authors.initials: C
authors.lastname: Zhou
authors.forename: Ruixiang
authors.initials: R
authors.lastname: Sun
authors.forename: Haipeng
authors.initials: H
authors.lastname: Wang
authors.forename: Chao
authors.initials: C
authors.lastname: Liu
authors.forename: Zuofei
authors.initials: Z
authors.lastname: Yuan
authors.forename: Liyun
authors.initials: L
authors.lastname: Xiu
authors.forename: Si-Min
authors.initials: SM
authors.lastname: He
mesh_terms: D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D013058:Mass Spectrometry; D051379:Mice; D008970:Molecular Weight; D010748:Phosphopeptides / Q000737:chemistry*; D010766:Phosphorylation; D011506:Proteins / Q000737:chemistry*; D057386:Search Engine
chemical_list: D010748:Phosphopeptides; D011506:Proteins