SimTandem is freely available without any warranty. If you use SimTandem in your work, please, cite us using the following publication:

Jiri Novak, Timo Sachsenberg, David Hoksza, Tomas Skopal and Oliver Kohlbacher. On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications. Journal of Integrative Bioinformatics, 10(3):228, 2013. Download citation: [ris], [bib]

SimTandem v. 1.1.96 (Windows 7 - x64, OpenMS 1.11) - download
SimTandem v. 1.1.96 (Linux - x64, OpenMS 1.11) - download

  • E-values are calculated for each PSM to enable the support of ConsensusID
  • aa_before and aa_after are reported in the output *.IdXML file for each peptide hit
  • X, C, Z, AX and CZ fragment ion series in theoretical spectra are supported
  • -ini and -write_ini parameters are supported thus SimTandem is visible like an internal TOPP tool in TOPPAS under Identification/SimTandem

SimTandem v. 1.1.74 (Windows 7 - x64, OpenMS 1.11) - download
SimTandem v. 1.1.74 (Linux - x64, OpenMS 1.11) - download

  • OpenMS 1.11 is now supported

SimTandem v. 1.1.65 (Windows 7 - x64, OpenMS 1.10) - download
SimTandem v. 1.1.65 (Linux - x64, OpenMS 1.10) - download

  • Linux is now supported
  • a bug was fixed when FileConverter was used as a predecessor of SimTandem

SimTandem v. 1.1.56 (Windows 7 - x64)

  • non-specific N-terminal and C-terminal variable modifications are now supported (use X to define a non-specific terminal modification (e.g., X(Acetyl)N-term+42.010565;)
  • the list of digestion enzymes has been extended

SimTandem v. 1.1.44 (Windows 7 - x64)

  • memory optimizations when many variable modifications are being searched
  • N-terminal and C-terminal modifications are now supported (when an amino acid is specified, e.g., "Q(Gln->pyro-Glu)N-term-17.026549;")

SimTandem v. 1.1.21 (Windows 7 - x64)

  • OpenMS 1.10 is now supported
  • SearchParameters in an output IdXML file were fixed
  • fixed bug: maxVariableModificationsPerSpectrum were not applied occasionally
  • fixed bug: lists of variable and fixed modifications had to end with a semi-colon

SimTandem v. 1.0.804 (Windows 7 - x64)

  • last version for OpenMS 1.9


Contact information

Jiri Novak
SIRET Research Group
Department of Software Engineering
Faculty of Mathematics and Physics
Charles University in Prague
Malostranske nam. 25
118 00 Prague
Czech Republic

novak [at]