Dear Yong, There are several MS-specific programs that I know of but they're not in the public domain. I have a couple of crude PERL scripts for this and an Excel application written by a former colleague. These are too crude to send out, but I would be happy to run your sequences and masses through them for you.
How accurately were the masses determined (hopefully using ESI LC MS and not MALDI-TOF, since the mass accuracy of the latter is not as good)? Do the two masses add up to the total m.w. of the starting protein? If they don't add up this likely means that either a) there are smaller fragments that you're not detecting or b) your original m.w. is not what you expect. I assume you also ran the original protein MS in the same way as the fragments? Is the original protein homogenous? If it is not this makes life quite difficult. Finally, since the two fragments associate tightly enough to co-elute on sizing this probably means that you've cut into an exposed loop or a linker region between tightly associated domains. Best regards, Artem -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yong Tang Sent: Saturday, March 31, 2007 1:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] (bigger) fragment identification of limited proteolysis w/ mass-spec Dear all, just a super dummy question: I treated a protein with trypsin, found the protein being degraded into two well-define fragments, ran a sizing column to find them co-elute, sent the peak fraction for mass-spec, got the two masses. Now here is the question - is there any program readily available for me to roughly identify these two (around 20K) fragments with the full-length sequence and these two masses, and of cause, with the fact that I use trypsin to cut it? I checked a lot of programs listed on Expasy to find them mostly dealing with smaller peptide length. Any information would be highly appreciated. Thanks and have a nice weekend, -yong
