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:

The first and third are values taken from the literature (references in the on-line help and the manual). The second option is based on the values for free amino acid residues. The fourth and last option is based on the definitions in the currently selected mass file and has to be checked in order to use these values.

Where are these values used?
The pI values are calculated for a protein and a peptide in their respective information dialog boxes (from the protein or peptide window, you select ‘Protein/peptide information’).
pI values are calculated in the peptide window if the column option is selected.
The simulated 2-D gel use pI calculations.
In the DigestAlyzer you can select pI as one axis option.
When reporting charges, as in the peptide window.
The charge vs. pH window, both when called from the protein and the peptide window.

Current limitations:
If a charged residue is modified, the original pKa value is still calculated as part of the total pI/charge. If a non-charged residue is changed to a charged residue and a pKa value specified, the calculations are ‘correct’.
If a terminal is modified, it still contributes to the pI/charge.

Specifying pKa values.

Site last updated: June 05, 2024