Electrophoresis is commonly used to separate proteins on the basis of size and/or charge. Typically, a sample containing target proteins is loaded into a porous matrix and voltage is applied. The proteins in the sample will migrate through the matrix at different velocities based on their varying size and charge.
At the end of the separation, the proteins can be detected as bands located at different vertical positions in the matrix. The matrix can be composed of a number of different materials, including paper, cellulose acetate, or gels made of polyacrylamide, agarose, or starch.
Polyacrylamide gels are the most commonly used matrices for the separation of proteins in a process called polyacrylamide gel electrophoresis (PAGE).
Since a protein’s net charge will affect its mobility in an electric field, the detergent sodium dodecyl sulfate (SDS) is usually added to denatured protein samples and buffers. This confers a negative charge to proteins roughly in proportion to polypeptide length, ensuring that mobility depends primarily on molecular mass and not charge.
Native (non-denaturing) gel electrophoresis is run in the absence of SDS, and thus the mobility of proteins depends on both charge and hydrodynamic size.