Two types of buffer systems can be used:
Continuous buffer systems — use the same buffer (at constant pH) in the gel, sample, and electrode reservoirs. Samples are loaded into wells, and proteins that are closer to the gel enter first. This provides a uniform separation matrix, but yields fuzzy and unresolved protein bands. Continuous systems are rarely used for protein electrophoresis but commonly used for nucleic acid analysis
Discontinuous buffer systems — use a gel separated into two sections (a large pore stacking gel on top of a small pore resolving gel, see figure below) and different buffers in the gels and electrode solutions. Proteins migrate quickly through the large pore stacking gel and then are slowed as they enter the small pore resolving gel. The proteins stack on top of one another to form a tight band, which helps improve resolution. Discontinuous buffer systems provide higher resolution than continuous systems, and varying the buffers used in the sample, gel, and electrode chambers creates a variety of discontinuous buffer systems that can be used for a variety of applications