Abstract: The present invention includes novel isoelectric focusing cells and methods for isoelectric focusing of amphoteric substances within fluids containing carrier ampholytes which inhibit the phenomena known as spiking or acid notching. The apparatus includes a barrier separating the electrode compartments from the focusing cell compartments which minimizes hydrogen and hydroxyl ions contained in electrolyte solution within the electrode chambers from passing into the focusing cell passageways. The currently preferred barrier is a bipolar membrane; however, the combination of anion and cation selective membranes is also effective. Such a barrier enables very narrow pH gradients to be established and maintained, thereby permitting high resolution separations of amphoteric biological substances.