Hi everyone,
I am working on a medicinal plant protein belonging to the Brassica family and I have run LC/MS/MS of tryptic peptides digested in solution and trying to find out the results through MASCOT, but unfortunately the protein sequence database (of my interest) is absent in Mascot thus giving low probability scores. I found genome database of Brassica. Is there any procedure in which I can compare these two i.e. Brassica genome with that of MS/MS results?
Your data would work best with annotated genome or transcriptome rather that raw reads. Have you tried these https://www.ncbi.nlm.nih.gov/assembly/?term=Brassica
Even better, perhaps, to download the species protein database from NCBI https://www.ncbi.nlm.nih.gov/protein/?term=Brassica.
Best of luck with your research.
Elena
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