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?
By the way,
chainsawfrom Proteowizard might be useful for digestion: http://proteowizard.sourceforge.net/tools/chainsaw.html
Thanks. I'll add it to my post, as
chainsawmight be more convenient in some cases
Would this take care of the simulation part?
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).