Precursor and Fragment charge values

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Sam Whedon

Sep 12, 2023, 11:01:59 AM9/12/23
to Comet ms/ms db search support

I am trying to analyze middle-down mass spec data using Comet along with the Trans-Proteomic Pipeline. My MS2 data comes predominantly from +7 to +10 precursors, and infrequently contains +6 fragments.
I have been using the pre-compiled comet.linux.exe on a cluster. I was wondering whether I can change the hard limit on +9 charge state precursors and +5 charge state fragments. Would it be sufficient to change the MAX_FRAGMENT_CHARGE and MAX_PRECURSOR_CHARGE values in CometData.h, and then compile?


Jimmy Eng

Sep 13, 2023, 3:35:37 PM9/13/23
to Comet ms/ms db search support
Hi Sam.  Yes, changing those two defines and re-compiling would lift those limits.  There's also MAX_PEPTIDE_LEN and MAX_PEPTIDE_LEN_P2 in CometDataInternal.h, the latter is 2 larger than whatever you set the former to, which define the maximum peptide length supported.  So consider expanding those as well if middle-down means larger than peptides of length 64.  I feel obligated to state that you're stepping into uncharted territory so it's possible/likely that expanding these values will break something that I can't anticipate right now.  But definitely give it a shot and follow-up with me (here or emailing me directly) if you notice any issues; I'll try to help address them as they come up.


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