What kind of "size" does SDS-PAGE separate by?
The protocol for SDS-PAGE uses a solution of sodium dodecyl sulfate (SDS, also known as lauryl sulfate) to solubilize and linearize folded protein molecules and give them a negative charge that is approximately proportional to the length (and more or less to the mass) of the protein, depending on its sequence. Some sequences may bind the SDS more readily, while others may not, so the relationship between charge and mass/length is not perfect.

The linearized (and often reduced, typically with DTT or &beta;-mercaptoethanol) protein solution is separated by polyacrylamide gel electrophoresis (PAGE), wherein the negatively-charged protein(s) migrate though the pores in a gel due to an electrical field applied across the gel. Smaller proteins run faster, and are visualized (by many different methods) nearer to the bottom of the gel, whereas larger proteins are closer to the top. Typically, a standard molecular weight marker is run alongside the samples of interest so that approximate molecular mass can be gauged. A number of situations may cause the samples to not migrate exactly according to their calculated molecular mass, including high levels of glycosylation, phosphorylation, or other post-translational modifications, as well as variable binding to the SDS as discussed above.