How can I do mass spectra in silico

Question

[Zhenbo]

My proteomics lab is considering a new approach for peptide tag assembler. Before doing it in wet lab, I'd like to validate it in silico.

It includes 3 steps (all in silico):
1. Enzyme digestion (with tools like PeptideMass, chainsaw),
2. Simulate mass spectra, expected output
3. Assemble the peptide tags

Any ideas to get expected output?

[manuel.belmadani]

By the way, chainsaw from Proteowizard might be useful for digestion: http://proteowizard.sourceforge.net/tools/chainsaw.html

[Zhenbo]

Thanks. I'll add it to my post, as chainsaw might be more convenient in some cases

[manuel.belmadani]

Would this take care of the simulation part?

http://bioinfo.ict.ac.cn/OpenMS-Simulator/

This might be useful for assembly, https://github.com/warrenlr/PASS some of the outputs look similar to the example you provided (with some differences, e.g. using sequence name instead of peptide in the first column).

Answer 1

[Zhenbo]

I found a solution: OpenMS

It is very simple. The standalone installer has all the function needed.

After installation, create a new workflow with three parts, <Input files>, Utils->MSSimulator, <Output files>

The output spectra data is in mzML format, which can be imported into PEAKS Studio and other software for further analysis.

Cite: MSSimulator: Simulation of Mass Spectrometry Data
Chris Bielow, Stephan Aiche, Sandro Andreotti, and Knut Reinert
Journal of Proteome Research 2011 10 (7), 2922-2929
DOI: 10.1021/pr200155f