The ELF Preparative Electrophoresis System for Size-Based Proteome Fractionation

Although the resolution of LS-MS systems is improving every year, size fractionation of complex samples prior to MS analysis is still very useful for many proteomic studies. Despite the promise of automated 2D LC systems, SDS PAGE remains a popular, but laborious, pre-fractionation method for MS. This poster demonstrates an automated preparative electrophoresis system (the ELF system) to fractionate complex protein samples into 12 contiguous size fractions. The system uses a two-dimensional process: first, proteins are electrophoresed through an SDS agarose gel column to separate the proteins by size, and second, the separated proteins are electrophoresed sideways out of the agarose column into a linear array of membrane-bounded elution modules that are positioned alongside the separation gel column. The fractionated samples are recovered in SDS buffer, and can be processed for LC-MS using commercial detergent removal spin columns and standard trypsin digestion methods.