Sodium dodecyl sulfate polyacrylamide electrophoresis (SDS-PAGE) is one of the most widely used methods to carry out analytical separations of small poly-peptides and proteins. Despite its recognized importance, our understanding of the transport of surfactant denatured proteins during electrophoresis is based greatly on assumptions of protein conformation inside the gel and on macroscopic measurements of their mobility. Contrast-variation SANS is used to provide, for the first time, a structural picture of the conformation of protein-surfactant complexes during this separation. Our recent SANS observations are discussed and related to transport models (Ogston model and reptation model) that have been proposed to occur during SDS-PAGE. The SANS technique is also applied to the analysis of alternative anionic surfactants to optimize separation efficiency based on the fundamental nano-structure of the complex.