Starting from version 6.20 of GPMAW, it is possible for the user to define pKa values for modifications, and from 6.21 also in the regular mass table.
How are these pKa values then used by GPMAW? For the modifications, it is quite simple, as the pKa values is taken into the calculations of pI and charge whenever it is defined in a sequence (i.e. whenever a residue is modified with the relevant modification).
However, for the mass file you have to specifically tell GPMAW to use the user-defined table, as GPMAW is able to use four different tables. To switch between these tables, enter the System setup, and on the first page of the dialog box you will find the following selection: