The pKa values (C: 8.3, D: 3.9, E: 4.3, H: 6.0, K: 10.5, R: 12.5, Y: 10.1, N-terminus: 9.6, Cterminus: 2.4) listed in were used to numerically calculate zeroth-approximation pI values, leveraging the Henderson-Hasselbalch equation. Labels were defined as the difference between these baseline values and the experimental pI values. Graph neural networks were trained using the root-mean-squared error (RMSE) as the loss function.