SDS-PAGE is used for separation of proteins or protein fragments based on their size. SDS is an ionic detergent that denatures and binds to proteins. Consequently, the proteins are negatively charged. An electric current is running through the gel in the electrophoresis with positive pole on the bottom. Since proteins are negatively charged, they migrate toward the positive pole of the gel. Some of the proteins are smaller so they can travel more quickly through the gel than the bigger proteins.