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.
