Comet parameters for variable modification

[Nachiket W]

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 

[Jimmy Eng]

Nachiket

The variable modification parameters in Comet are definitely confusing/complex.  For search parameters documentation, you can check out the Parameters page on the Comet website.  And specifically here's the help page for the variable_modXX 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.

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 as each is described there.  Please follow-up here or (on Comet's Google Group) if you have any additional questions.

Jimmy

[Nachiket W]

Thanks alot Jimmy! I read through some of the resources and they are very helpful. Very grateful for your help!

Sincerest thanks,

Nachiket 

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