I have been trying to analyze PTMs of some files in TPP through PTM prophet, using the files of the comet search, it is giving the results of peptides but shows failure even every time for the PTM ....
I am a beginner level Student, so it is hard to figure out where I am going wrong, if you can help me I would be grateful. I have attached a ppt of step I took ,
Phospho PTM is edited in my parameter file .
Proteomics lab , IIT Bombay