Hi, I am trying to set-up the TPP to run an X!Tandem search. I've read Jimmy Eng's tutorial on using X!Tandem within the TPP. The problem I'm having is editing the X!Tandem parameters file. Should I be editing the default parameters file (tandem_params) in the parameters folder? Or should I be creating a new parameters file in the data folder? I'm trying to search data that needs the enzyme set to Lys-C and I can't seem to find the protein cleavage input in the default params file.
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