Question about "add_C_cysteine" Parameter and output format

[Jannik Schneider]

Hello everyone,

I have a question regarding this parameter. Is it true that cysteine is now always considered with this static modification? Since in my output (I did a rescoring with percolator) the modification is not explicitly shown. So can I assume that I can add a "+57.0215" after every occurence of a C inside the string, when comparing it with other search tool outputs?

Thanks for your time and help  

[Jimmy Eng]

Alkylation by iodoacetamide of free cysteines is pretty common in mass spec experiments.  That being said, there are different samples, experiments, sample prep workflows, etc. where this is not the case.  Which means it's not true that this +57 cysteine modification is applied as a static mod for every dataset in existence.  If you want/need to be thorough, you should confirm that this static modification was applied in the underlying database search for the datasets you're analyzing.  Hopefully others can chime in if you're looking for more feedback.  There aren't a lot of good groups/forums to ask question like this ... maybe the /r/proteomics community on reddit if you want a wider audience for non Comet-specific questions as it has ~10X more members than this little group.