Since Cys is almost always alkylated with iodoacetamide in most experiments:
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Correct, if you did not use iodoacetamide, then change it to 0.0
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I’m not certain I understand your question. If you’re looking for a template X!Tandem params file, there should be one in your installation in the data/params folder. There should be a tandem_params.xml? In the same folder as the template comet.params? Do you have that?
Eric
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