Inference of Peptides with numeric representation of PTMs

[think-o]

I have used MzidtoTsv Converter for the MS/MS peptide profiles (mzml files) I have had. I did not use any modification file for -mod and run the tool moslty with the default parameters. I would like to know understand more about the numeric representation of the carbamidomethylation as it not so much elaborative in the readme.md file. Was the PTM represented for every occurrence of cysteine in the peptide? I would like to know about the standard PTM as mentioned in the tool description.

[FarmGeek4Life]

Note that the documentation for MS-GF+ at https://msgfplus.github.io/msgfplus/MSGFPlus.html states the following:

-mod ModificationFile (Default: standard amino acids with fixed C+57, though only if -mod is not specified)

• Modification file name. ModificationFile contains the modifications to be considered in the search.
• If -mod is not specified, standard amino acids with fixed Carbamidomethylation C will be used.
• See an example MS-GF+ modification file.

If you really want no modifications, I believe you need to create an empty text file and provide that to MS-GF+ with -mod