I am currently involved in an MS/MS cataloging of proteins from a eukaryotic microbe. I want to map the peptide data generated from MASCOT searches to the FASTA format protein sequences in my database. The MS/MS experts that I am collaborating with have apparently never done this before, however, so they can't tell me how to do this (I am not a mass spectrometrist). Is there any free software/scripts that I can use to extract significant/high-scoring peptides and map them onto a sequence, preferably bolded and in a color other than black?
Thanks for your help!