Defined buffer systems have been considered by researchers as replacements for synthetic carrier ampholyte mixtures in IEF in order to reduce both costs and deleterious protein-ampholyte interactions. In this paper, a mathematical model for the behavior of two-component pH gradients during IEF is applied to a vortex-stabilized electrophoresis apparatus. Equations for mass conservation, molar fluxes, and the electric field describe the behavior of the components in the electric field. Equilibrium constants are used in the model to account for interconversion between the positive, negative, and neutral states for each component. The model was applied to predict pH gradients using two different defined buffer systems. The model's predictions fell within the 95% confidence interval of a least-squares fit to the experimental pH gradients except in the regions near the ends of the pH gradients, where large pH excursions occurred during the experiments.