Question on multi phosphorylated peptides #11
Description
I was just wondering, since MaxQuant's Phospho (STY)sites.txt file comes with three columns per sample (__1, __2, __3)--an individual column for singly, double, and triply phosphorylated peptides, how did you deal with that? I see that your pre-processsing steps ask for and assume that each column is a different sample, but how did you deal with the 3 columns per sample output format of MaxQuant? Thank you for providing such a great resource!