English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

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.

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