Omit peptides containing Cys

[patrick-willems]

Dear MSstats team,

I was wondering whether there would be an easy argument to provide in the MaxQtoMSstatsFormat function to indicate to skip cysteine-containing peptides (I do not want to use these for label-free quantification)? I saw there was for instance also the argument 'RemoveOxidationMpeptides', hence perhaps some additional argument could be used? Or would it be as simple as trimming down the evidence table?

Thanks in advance Patrick

[mstaniak]

Or would it be as simple as trimming down the evidence table?

correct, it's easiest to just remove such peptides before applying our converter

[patrick-willems]

Ok thanks! Just to be sure.