  Electrophoretic separations of proteins are widely used in proteomic
analyses, and rely heavily on SDS electrophoresis. This mode of separation is
almost exclusively used when a single dimension separation is performed, and
generally represents the second dimension of two-dimensional separations.
Electrophoretic separations for proteomics use robust, well-established
protocols. However, many variations in almost all possible parameters have been
described in the literature over the years, and they may bring a decisive
advantage when the limits of the classical protocols are reached. The purpose
of this article is to review the most important of these variations, so that
the readers can be aware of how they can improve or tune protein separations
according to their needs. The chemical variations reviewed in this paper
encompass gel structure, buffer systems and detergents for SDS electrophoresis,
two-dimensional electrophoresis based on isoelectric focusing and
two-dimensional electrophoresis based on cationic zone electrophoresis.
