Can I solve my problem with Mascot/FIndPept...? - (Oct/05/2011 )

Hi,

I am a researcher in the bio-inorganic chemistry domain, developing artificial proteases. I cut proteins with inorganic compounds and want to find out where I cut them...
At this point I am struggling with MS analysis programs.
What I can do with most programs: masses obtained from MS + protease (most of the time trypsin) = protein from which fragments originate
What I want to do in stead: masses obtained from MS + sequence of protein from which fragments originate = possible matches of masses to sequence of known protein ==> where was the protein cut (most likely)
Does anyone have any idea if the existing MS programs can handle what I want to do? And if not, is there a mathematical program that can scan a protein sequence (with known masses for each AA) and find the best matches of the masses (of the cleavage fragments) I find with MS to this sequence?
Any suggestions and advices are welcome...

Thanks in advance,
KS

Cannot understand what you want to do. Please described in more detail.