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

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...

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Autores principales: Wang, Yaojun, Yang, Fei, Wu, Peng, Bu, Dongbo, Sun, Shiwei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415337/
https://www.ncbi.nlm.nih.gov/pubmed/25887925
http://dx.doi.org/10.1186/s12859-015-0540-1
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author Wang, Yaojun
Yang, Fei
Wu, Peng
Bu, Dongbo
Sun, Shiwei
author_facet Wang, Yaojun
Yang, Fei
Wu, Peng
Bu, Dongbo
Sun, Shiwei
author_sort Wang, Yaojun
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0540-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-44153372015-05-01 OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction Wang, Yaojun Yang, Fei Wu, Peng Bu, Dongbo Sun, Shiwei BMC Bioinformatics Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0540-1) contains supplementary material, which is available to authorized users. BioMed Central 2015-04-02 /pmc/articles/PMC4415337/ /pubmed/25887925 http://dx.doi.org/10.1186/s12859-015-0540-1 Text en © Wang et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Wang, Yaojun
Yang, Fei
Wu, Peng
Bu, Dongbo
Sun, Shiwei
OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
title OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
title_full OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
title_fullStr OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
title_full_unstemmed OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
title_short OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction
title_sort openms-simulator: an open-source software for theoretical tandem mass spectrum prediction
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415337/
https://www.ncbi.nlm.nih.gov/pubmed/25887925
http://dx.doi.org/10.1186/s12859-015-0540-1
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