A procedure for the analysis of glycoproteins and glycopeptides using the PhastSystem with detection by the periodic acid-Schiff stain is described. Following sodium dodecyl sulfate or nondenaturing polyacrylamide gel electrophoresis and also isoelectric focusing, samples are stained directly for the presence of carbohydrates. By using the PhastSystem, the method is rapid, sensitive, reliable and allows storage of the gels without a change in the stain. As little as 0.1 micrograms of protein-associated carbohydrates can be detected. The staining procedure is also used following isoelectric focusing of mucin-derived glycopeptides to visualize their charge differences and the increase of their isoelectric point after neuraminidase treatment.