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Updated Setting the Parameters (markdown)
Update the default value of write_calibrated_mgf
Add more explanations to decoy_prefix.
Add more explanation to decoy_prefix parameter.
Update some parameters according to 2.3.
Add write_calibrated_mgf. Change allow_multiple_variable_mods_on_residue's default value to 0. Improve a description.
add link to parameter files
Add three new parameters.
linked to list of enzymes on PeptideProphet page of Philosopher wiki
Add excluded_scan_list_file parameter.
precursor_charge description
Change the explanation about the precursor_charge
routine