Hello, I want to have two constant modification in a particular amino acid. To be more specific- the concerned amino acid should compulsorily have one of the two constant modification. Can anyone please suggest me the best way to do it in comet. In regular search, my understanding is- only one constant modification is allowed for one amino acid. One way I could think of doing it is to modify the mass of the concerned amino acid (average as well as monoisotopic) with the smaller of the two mass modification and then have the difference between the two as the constant mass modification. This way we would have to define only one constant modification in the parameter file. However, I would have to change the default mass of the concerned amino in the amino acid mass library file. Can anyone help me to locate this library file in TPP?
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