Comet fixed and variable modifications

[Francesco Demetrio Lofaro]

Hello,

i need to set these modification in Comet parameters: 1) fixed modification: Carbamydomethyl (N-term); 2) variable modifications: Oxidation (M); Deamidated (NQ).

Thank you for your help,

Francesco

[Jimmy Eng]

Carbamidomethylation has a modification mass of 57.021464.  To apply it to each peptide's n-termini if that's your intent:

   add_Nterm_peptide = 57.021464

This modification is commonly applied to cysteine residues:

   add_C_cysteine = 57.021464

For methionine oxidation as a variable modification, use the "variable_mod*" parameters:

   variable_mod01 = 15.9949 M 0 3 -1 0 0 0.0

For deamidation:

   variable_mod02 = 0.984016 NQ 0 3 -1 0 0 0.0

A description of each of the parameters, particularly the crazy list of settings for the variable_mod parameters, can be found here:

   http://comet-ms.sourceforge.net/parameters/parameters_201901/

Good luck.

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