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MSSimulator

A highly configurable simulator for mass spectrometry experiments.

This implementation is described in

Bielow C, Aiche S, Andreotti S, Reinert K
MSSimulator: Simulation of Mass Spectrometry Data
Journal of Proteome Research (2011), DOI: 10.1021/pr200155f

The most important features are:

Look at the INI file (via "MSSimulator -write_ini myini.ini") to see the available parameters and more functionality.

Input: FASTA files

Protein sequences can be provided as FASTA file. We allow a special tag in the description of each entry to specify protein abundance. If you want to create a complex FASTA file with a Gaussian protein abundance model in log space, see our Python script shipping with your OpenMS installation (e.g., <OpenMS-dir>/share/OpenMS/examples/simulation/FASTAProteinAbundanceSampling.py). It supports (random) sampling from a large FASTA file, protein weight filtering and adds an intensity tag to each entry.

If multiplexed data is simulated (like SILAC or iTRAQ) you need to supply multiple FASTA input files. For the label-free setting, all FASTA input files will be merged into one, before simulation.

For MS/MS simulation only a test model is shipped with OpenMS.
Please find trained models at: http://sourceforge.net/projects/open-ms/files/Supplementary/Simulation/.

To specify intensity values for certain proteins, add an abundance tag for the corresponding protein in the FASTA input file:

e.g.

>seq1 optional comment [# intensity=567.4 #]
ASQYLATARHGFLPRHRDTGILP
>seq2 optional comment [# intensity=117.4, RT=405.3 #]
QKRPSQRHGLATARHGTGGGDRA

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.2.0 Documentation generated on Wed Jul 12 2017 10:28:39 using doxygen 1.8.13