Since Mascot uses the Unimod file to store modifications, when you add custom modifications in Mascot, this file,
mascot/config/unimod.xml (http://www.matrixscience.com/mascot_support_v2_5.html), is edited. Note that depending on how your Mascot server is configured the Unimod file might be in a different location or have a different name -- speak to your Mascot Server administrator for details.
You will need to fetch the updated modifications file from the Mascot server and then apply it in Scaffold, according to the instructions on page 82:
Here is some general information on Unimod: