Prepare the sample solution and the standard solution of known molecular weight.
Prepare a buffer solution with the nearest pH value to your sample.
Prepare the supporting medium (gel); common gel-forming materials are polyacrylamide, a water-soluble, cross-linked polymer, agarose and polysaccharide.
Place the gel between electrode compartments, with the bottom selected as anode or cathode, depending on whether anions or cations are being separated.
With a pipette, carefully drop a little amount of solution of each sample into one of several precast notches on top of the gel.
Add glycerol and a water-soluble tracking dye to the sample. The glycerol makes the sample solution dense, so that it does not mix into the buffer solution in the upper electrode chamber.