title: OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction.
abstract: BACKGROUND
  Tandem 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  OpenMS-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.
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China. wangyaojun@ict.ac.cn.|University of Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100049, China. wangyaojun@ict.ac.cn.
authors.forename: Yaojun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China. yangfei@ict.ac.cn.|University of Chinese Academy of Sciences, 19A, Yuquan Road, Beijing, 100049, China. yangfei@ict.ac.cn.
authors.forename: Fei
authors.initials: F
authors.lastname: Yang
authors.affiliation: Institute of Biophysics, Chinese Academy of Sciences, 15, Datun Road, Chaoyang District, Beijing, 100101, China. wupeng@moon.ibp.ac.cn.
authors.forename: Peng
authors.initials: P
authors.lastname: Wu
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China. dbu@ict.ac.cn.
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.affiliation: Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6, Kexueyuan South Road, Zhongguancun, Beijing, 100190, China. dwsun@ict.ac.cn.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D016208:Databases, Factual; D006801:Humans; D008962:Models, Theoretical; D010446:Peptide Fragments / Q000032:analysis*; D011506:Proteins / Q000032:analysis*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D011506:Proteins