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Question: How can I do mass spectra in silico
2
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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?

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0

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

ADD REPLYlink 11 months ago
manuel.belmadani
• 830
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Thanks. I'll add it to my post, as chainsaw might be more convenient in some cases

ADD REPLYlink 11 months ago
Zhenbo
• 20
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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).

ADD REPLYlink 11 months ago
manuel.belmadani
• 830
0
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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

ADD COMMENTlink 10 months ago Zhenbo • 20

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