Comet parameter: sample_enzyme_number

• Note that this parameter has no effect on the search and search results at all. It is used solely to annotate additional information in the output.
• This parameter is relevant only for pepXML output i.e. when “output_pepxmlfile” is set to 1.
• The pepXML format encodes the enzyme that is applied to the sample i.e. trypsin. This enzyme is written to the “sample_enzyme” element.
• The sample enzyme could be different from the search enzyme i.e. the sample enzyme is “trypsin” yet the search enzyme is “Cut_everwhere” for a non-specific search. Hence the need for this separate parameter.
• Valid values are any integer represented in the enzyme list.
• The default value is “0” if this parameter is missing.

Example:

sample_enzyme_number = 1
sample_enzyme_number = 3