... mass ratio should not change with size. In solution (water), in principle all different sized proteins covered with SDS would run through an inert polymer, polyacrylamide. The density and pore size of this polymer can be varied by just how you make it. Thus, the size of molecules that can pass through the matrix can be varied. This determines what molecular weight range the gel will have the highest resolving power. Native Gels: It is also possible to run protein gels without SDS. These are called native gels in that one does not purposely denature protein. Here, the native charge on the protein (divided by its mass) determines how fast the protein will travel and in what direction. Electrofocusing Gels: Another variation of gel electrophoresis is to pour a gel that purposely has a pH gradient from one end to the other. As the protein travels through this pH gradient, its various ...

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