Question: How can I do mass spectra in silico
1
gravatar for Zhenbo
7 days ago by
Zhenbo10
Boston
Zhenbo10 wrote:

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?

ADD COMMENTlink modified 7 days ago • written 7 days ago by Zhenbo10

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

ADD REPLYlink written 7 days ago by manuel.belmadani570

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

ADD REPLYlink written 7 days ago by Zhenbo10

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 written 6 days ago by manuel.belmadani570
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