Enriching basic and acidic rat brain proteins with ion exchange mini spin columns before two-dimensional gel electrophoresis.

Abstract

Proteome analysis by two-dimensional gel electrophoresis (2-DGE) faces significant challenges because of the complexity of biological samples. However, the complexity of a protein sample can be reduced prior to 2-DGE by applying protein fractionation. Protein fractionation allows analysis of one protein subset at a time, thereby, increasing the load of proteins of interest, enriching low-abundance proteins, and increasing the resolution of protein spots on a 2-D gel.Here we describe an ion exchange chromatography based method--the use of anion or cation exchange (AEX or CEX) mini spin columns--for sample fractionation. Using rat brain tissues, we demonstrate that these mini spin columns provide an easy, convenient, and reproducible way of fractionating brain proteins to enrich basic or acidic proteins before 2-DGE.