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

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?

This might be useful for assembly, 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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