#massspecsos Best way/software for peptide mapping from limited proteolysis or full proteolysis experiments for a single, purified recombinant protein? Something that I can use/search against the Fasta for so the search would be our protein and contaminants with Thermo data.

Thanks guys for the fast replies! I appreciate you all!

For a limited set of proteins, we just target the expected peptides. It's not the search, it's which peptides are more quantitatively stable because of the protease protection.

Thermo Biopharma Finder can search data against a single protein sequence.. Not sure how it works for limited proteolysis samples though..

Hi Tonya. I think metamorpheus can help you. If you are interested we can have a chat about it. I’d be happy to help

For DDA data on a purified protein, I used to use a software called Morpheus. I don't think it's maintained anymore, but it worked well right out of the box.