As one might expect, running samples on a protein gel is very similar torunning samples on a nucleic acid gel. The sample is prepared by dilutingit into a concentrated sample loading buffer so that the loading bufferis at a final concentration of 1X. The samples are then heated at 900Cfor 3 minutes and then loaded onto the gel, which is not pre-run priorto sample loading. Protein gels are run more slowly than nucleic acid gels,and consequently may require more time. A gel 20 cm in length generallyruns for about 3-4 hours. The time required is of course variable dependingon the nature of the sample. The samples are run into the stacking gelat about 2-3 watts for 30 minutes or so, after which the power is increasedto 8-10 watts until completion. I always include on the gel a lane thatcontains pre-stained molecular weight markers, which serve two purposes:(1) they allow you to monitor the gel, providing an indicator of how thegel is running, and (2) provide molecular weight indicators so that youcan determine how long to run the gel.