In the Scaffold DIA user guide, you can find the following excerpt on page 41:
Digestion Enzyme - Enzyme used to digest proteins. If the correct enzyme is not listed in the
dropdown, it is possible to read in a custom enzyme specification from a workflow file. For
assistance, please contact Proteome Software Support. If Non-specific is selected, the maximum
number of missed cleavages should be set to one less than the maximum peptide length.
To configure a custom digestion enzyme, you can add the following to the workflow file. As an example, this would use the Endoproteinase AspN (Asp-N):
DIGESTION-ENZYME=AspN;[X]|[D]