Hi TPP team, I got a silly question here about using comet and tandem to search TMT data within the TPP workflow. I didn't found anywhere in Comet and Tandem's parameter file to specify the quantitative method, so I simply put TMT as a fix modification on Nterm and K just for the search and use the Libra to do the quantitation later. It all went OK, but I just realize one confusion issue here: because the TMT was defined as a fix modification, how does Comet and Tandem know the TMT will be cleaved off during HCD that there is no TMT modificaiton in MS/MS spectrum?
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