Effect of pH and ionic strength of running buffer on peptide behavior in capillary electrophoresis: theoretical calculation and experimental evaluation.

The effect of pH and ionic strength of running buffer on peptide behavior in capillary electrophoresis (CE) is studied. A system for predictions of peptide migration in CE (SPPMCE) developed in our laboratory has been tested in a wide range of pH and buffer concentrations. The SPPMCE consists of a computer program for calculating peptide pKa values, an equation which relates peptide structures to their electrophoretic mobilities and a coupled computer program for the prediction of electropherograms. More than 25 different buffers have been employed, covering a pH range of 2-11 and a concentration range of 5-100 mM. Results from experiments are compared with the theoretical predictions. Good agreement is observed, which confirms the utility of the SPPMCE and allows fast and easy optimization of peptide separations in CE, with nothing more than the amino acid sequence of the linear peptide as the input.