A PTM that can happen on any residue?

[David Tabb]

Hi, Jimmy.  I am trying to identify a induced chemical modification (oxidation) that can occur on any amino acid in the peptide, with up to three occurrences per peptide.

I have tried two different configurations for this PTM, but it appears to be silently ignored by Comet in either configuration:
variable_mod01 = 15.9949 ACDEFGHIKLMNPQRSTVWY 0 3 -1 0 0 0.0

variable_mod01 = 15.9949 * 0 3 -1 0 0 0.0

Does Comet limit how many residues may carry a given mass shift?  Would it help if I listed the same mass on multiple variable_mod0x lines, each time adding another three amino acids?

Thanks,

Dave

[Jimmy Eng]

Hi David.  Sorry for the late reply ... I have yet to figure out why I don't get email notifications of every post so I just saw your post today after getting notification of a different post from today.

Staring at Comet code, there is a limit of 19 mass residues for the variable mod entry.  I had intended for that max limit to be 20 but I sadly didn't implement the limit correctly.  I do have a simple fix that will extend the modification residue list to the number of all possible residues that Comet supports.  If you'd like me to send you a patched binary, let me know what platform you use; Linux or Windows or both.  Or I can send you the patch if you compile Comet from sources yourself.  (And fwiw, the asterisk notation is not supported.)  Hope you're doing well!

Jimmy

[David Tabb]

Hi, Jimmy.

Thank you for your kind note and making a rapid fix to handle the "any AA" PTM case.  I have downloaded and tested Comet-v2023.01.0 with success!  This line now gives the correct behavior:

variable_mod01 = 15.9949 ACDEFGHIKLMNPQRSTVWY 0 3 -1 0 0 0.0

I believe that adding this functionality will be useful for people performing "FPOP" experiments.

Now I get to apologize for being slow.  Since your message, my wife and I have moved from France down to South Africa ("returning home").  We really missed this crazy place!

Thanks again,

Dave