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 "1" if this parameter is missing.

search_enzyme_number = 0     typically no-enzyme
search_enzyme_number = 1     typically trypsin

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

    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.