Thanks alot Jimmy! I read through some of the resources and they are very helpful. Very grateful for your help!
Sincerest thanks, Nachiket On Tue, Nov 12, 2024 at 10:00 PM Jimmy Eng <[email protected]> wrote: > Nachiket > > The variable modification parameters in Comet are definitely > confusing/complex. For search parameters documentation, you can check out > the Parameters page > <https://uwpr.github.io/Comet/parameters/parameters_202402/>on the Comet > website <https://uwpr.github.io/Comet/>. And specifically here's the > help page for the variable_modXX > <https://uwpr.github.io/Comet/parameters/parameters_202402/variable_modXX.html>entries. > The parameters documentation on the Comet website is always updated to the > latest Comet release which may be a bit newer than the version you're using > in the TPP; documentation for previous Comet releases can be found on the > Releases > page <https://uwpr.github.io/Comet/releases/>. > > For protein N-terminal acetylation, use: > > variable_mod02 = 42.010565 n 0 1 0 0 0 0.0 > > For peptide N-terminal acetylation, use: > > variable_mod02 = 42.010565 n 0 1 0 2 0 0.0 > > If you're interested in understanding what each of eight entries mean in > the variable_modXX entry, I encourage you to read through the help page > <https://uwpr.github.io/Comet/parameters/parameters_202402/variable_modXX.html> > as each is described there. Please follow-up here or (on Comet's Google > Group <https://groups.google.com/g/comet-ms>) if you have any additional > questions. > > Jimmy > > On Tuesday, November 12, 2024 at 2:33:59 AM UTC-8 Nachiket W wrote: > >> Hello, >> >> I am running an analysis that requires the inclusion of *N-terminal >> acetylation* as a variable modification. I am unable to understand the >> details that I should enter in each of the options mentioned in the format >> for variable mods (screenshot attached). >> >> Please help me understand the format and if possible share any sources or >> a manual that can help me identify the parameters that need to be set for a >> modification. >> >> Sincerely, >> Nachiket >> [image: Screenshot 2024-11-12 143322.png] >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion visit > https://groups.google.com/d/msgid/spctools-discuss/ed6e5e1f-ed5a-465d-aaa3-3b2f1456684cn%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/ed6e5e1f-ed5a-465d-aaa3-3b2f1456684cn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion visit https://groups.google.com/d/msgid/spctools-discuss/CAB-qBE_xgFxVojC5yp1_0cbxzYwHAek%2Be7qC2%2Becz601PLWZRQ%40mail.gmail.com.
