Hey all,
What could really make yhis program have significant advantages to SequestHT or Mascot would be the possibility to select how many of the same modifications one could have for individual ptms.
For example, I have max 4 mod and max 3 of the same but I am also looking to find C-nitrosylation sites, and since they are rare, i would like to be able to select only max 1 per peptide for this one specifically, whereas for S,T phoshorylation 3 max is not too much at all. This way more modifications can be meaningfully analyzed with the same compuattionall regirenments.
All the best,
David