Welcome to OpenMS-Simulator Site

OpenMS-Simulator implements a novel approach to predict the y-ion intensities of the theoretical spectrum for given peptide sequence. Compared with the existing theoretical spectrum prediction tool MassAnalyzer, OpenMS-Simulator not only simplifies the computation, but also improves the prediction accuracy.

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How OpenMS-Simulator will benefit you


OpenMS-Simulator predicts the y-ion intensities in the spectrum for given peptide, and the prediction accuracy is improved over MassAnalyzer.


OpenMS-Simulator can re-rank the reported peptides of SEQUEST and X!TANDEM to improve the correctly identified peptides number.


OpenMS-Simulator takes peptide file as input and outputs a MGF file that contains the predicted theoretical spectra, and the spectra can be viewed by OpenMS-Simulator directly.

OpenMS-Simulator Features

Accurate prediction of theoretical spectrum for peptide sequence by predicting the y-ion intensities.

Improved the accuracies of SEQUEST and X!TANDEM by re-ranking the identified peptide sequences reported by these two softwares.

OpenMS-Simulator can only support the CID and HCD fragmentation models for peptides with double charges and no PTMs.

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Simulator the Theoretical Spectra of Peptides

Your input should be a file that contains some peptides!
Peptide File (.fasta file):
Fragment Type: CID   HCD
Charge State: +1   +2   +3
   (OpenMS-Simulator can only support the CID and HCD fragmentation models for peptides with double charges.)
1. Sun S, Yang F, Yang Q, et al. MS-Simulator: Predicting Y-Ion Intensities for Peptides with Two Charges Based on the Intensity Ratio of Neighboring Ions[J]. Journal of proteome research, 2012, 11(9): 4509-4516. [PDF] [BibTex]
2.Wang Y, Yang F, Wu P, et al. OpenMS-Simulator: an open-source software for theoretical tandem mass spectrum prediction[J]. BMC bioinformatics, 2015, 16(1): 110. [PDF] [BibTex]


OpenMS-Simulator is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.

OpenMS-Simulator is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

You may copy and distribute verbatim copies of source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty.

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Contact Us

Key lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences

No. 6, Kexueyuan South Road, Zhongguancun, Beijing, China