Comet parameter: search_enzyme2_number

• The optional second search enzyme is specified by this parameter.
• If a second digestion enzyme is not applied, set this parameter value to 0.
• If a second enzyme is selected, both the first enzyme and this second enzyme will be applied to generate peptides.
• 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 from here in each search. 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_enzyme2_number = 0 (no second enzyme applied)
search_enzyme2_number = 10 (digest with chymotrypsin in addition to first enzyme)

The format of the parameter definition looks like the following:

[COMET_ENZYME_INFO]
0.  Cut_everywhere         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.