OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction

doi:10.1186/s12859-015-0540-1

	OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
	Wang,Yaojun 1,2; Yang,Fei 1,2; Wu,Peng 3; Bu,Dongbo 1; Sun,Shiwei 1
	2015-04-02
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	16 期号:1
摘要	AbstractBackgroundTandem mass spectrometry (MS/MS) acts as a key technique for peptide identification. The MS/MS-based peptide identification approaches can be categorized into two families, namely, de novo and database search. Both of the two types of approaches can benefit from an accurate prediction of theoretical spectrum. A theoretical spectrum consists of m/z and intensity of possibly occurring ions, which are estimated via simulating the spectrum generating process. Extensive researches have been conducted for theoretical spectrum prediction; however, the prediction methods suffer from low prediciton accuracy due to oversimplifications in the spectrum simulation process.ResultsIn the study, we present an open-source software package, called OpenMS-Simulator, to predict theoretical spectrum for a given peptide sequence. Based on the mobile-proton hypothesis for peptide fragmentation, OpenMS-Simulator trained a closed-form model for the intensity ratio of adjacent y ions, from which the whole theoretical spectrum can be constructed. On a collection of representative spectra datasets with annotated peptide sequences, experimental results suggest that OpenMS-Simulator can predict theoretical spectra with considerable accuracy. The study also presents an application of OpenMS-Simulator: the similarity between theoretical spectra and query spectra can be used to re-rank the peptide sequence reported by SEQUEST/X!Tandem.ConclusionsOpenMS-Simulator implements a novel model to predict theoretical spectrum for a given peptide sequence. Compared with existing theoretical spectrum prediction tools, say MassAnalyzer and MSSimulator, our method not only simplifies the computation process, but also improves the prediction accuracy.Currently, OpenMS-Simulator supports the prediction of CID and HCD spectrum for peptides with double charges. The extension to cover more fragmentation models and support multiple-charged peptides remains as one of the future works.
关键词	Mass spectrometry Theoretical spectrum prediction Peptide identification
DOI	10.1186/s12859-015-0540-1
语种	英语
WOS记录号	BMC:10.1186/s12859-015-0540-1
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4549
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Sun,Shiwei
作者单位	1.Chinese Academy of Sciences; Key Lab of Intelligent Information Processing, Institute of Computing Technology 2.University of Chinese Academy of Sciences 3.Chinese Academy of Sciences; Institute of Biophysics
推荐引用方式 GB/T 7714	Wang,Yaojun,Yang,Fei,Wu,Peng,et al. OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction[J]. BMC Bioinformatics,2015,16(1).
APA	Wang,Yaojun,Yang,Fei,Wu,Peng,Bu,Dongbo,&Sun,Shiwei.(2015).OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction.BMC Bioinformatics,16(1).
MLA	Wang,Yaojun,et al."OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction".BMC Bioinformatics 16.1(2015).