Protease Digestion

You can add custom proteases to MetaMorpheus by going to Data -> Open folder with mods/data files -> ProteolyticDigestion -> proteases.tsv.

Open this file with Excel (or a text editor). To create a new protease, give it a name and define its digestion rules using the following syntax:

Character(s)     Purpose
|                Defines cut site
[]               Defines amino acids preventing cleavage
X                Wildcard (any amino acid)
{}               Defines exceptions to the wildcard character
,                Delimits multiple cleavage motifs

Example Name               Syntax Example     Syntax Interpretation
Trypsin                    K|,R|              Cuts after K and R
AspN                       |D                 Cuts before D (i.e., the N-terminal side of D)
Trypsin no proline rule    K|[P],R|[P]        Cuts after K and R, except when the K or R is followed by a P
Collagenase                GPX|GPX            Recognizes the GPXGPX motif, and cuts after the first X
Example                    RRX{P}|            Recognizes the RRX motif, and cuts after the X unless the X is a P