## Comet parameter: search_enzyme_number

- The search enzyme is specified by this parameter.
- The list of search enzymes is specified at the end of the comet.params file beginning with the line `[COMET_ENZYME_INFO]`. The actual enzyme list and digestion parameters are read here. So one can edit/add/delete enzyme definitions simply be changing the enzyme information.
- This parameter works in conjection with the num_enzyme_termini parameter to define the cleavage rule for fully-digested vs. semi-digested search options.
- This parameter works in conjection with the allowed_missed_cleavage parameter to define the miss cleavage rule.
- The default value is "0" if this parameter is missing.

Example:
`search_enzyme_number = 0` typically no-enzyme
`search_enzyme_number = 1` typically trypsin

- The format of the parameter definition looks like the following:

      [COMET_ENZYME_INFO]
      0.  No_enzyme              0      -           -
      1.  Trypsin                1      KR          P
      2.  Trypsin/P              1      KR          -
      3.  Lys_C                  1      K           P
      4.  Lys_N                  0      K           -
      5.  Arg_C                  1      R           P
      6.  Asp_N                  0      D           -
      7.  CNBr                   1      M           -
      8.  Glu_C                  1      DE          P
      9.  PepsinA                1      FL          P
      10. Chymotrypsin           1      FWYL        P

  The first column of the parameter definition is the enzyme number. This number list must start from 0 and sequentially increase by 1. The second column is the enzyme name; no spaces are allowed in this name field. The third column is the digestion "sense" i.e. a value of "0" specifies cleavage N-teriminal to (before) the specified residues in column 4 and a value of "1" specifies cleavage C-terminal to (after) the specified residues in column 4. Column 4 contains the residue(s) that the enzyme cleaves at. Column 5 contains the flanking residue(s) that negate cleavage.