Current Strategies and Techniques for the Analysis of Low-Abundance Proteins and Peptides from Complex Samples

Hans   H.   von Horsten

Abstract

The dynamic detection range of proteomic analyses is limited by sample complexity. The investigation of low-abundance proteins requires a considerable enhancement of spot intensity which can be achieved by a strategic approach combining prefractionation and sample concentration. Chromatographic, electrophoretic and centrifugal separation techniques are very useful means to reduce sample complexity. Successful prefractionation strategies have resulted in the discovery of several previously undetected proteins. While many separation techniques have already been recognized as a powerful means of protein sample prefractionation and proteome enhancement, some interesting methods have yet to be evaluated. Most of the recent experimental approaches have used prefractionation as a major step towards the detection of lowabundance proteins. However, protein concentration techniques are another almost equally important means of spot intensity enhancement and detection of rare proteins. This review summarizes established and novel fractionation and concentration techniques for peptides and proteins and gives an outline of their recent successful application in the proteomic field.

Keywords: Electrophoretic separation techniques, vertical agarose gel electrophoresis, prefractionation approaches, nonequilibrium pH-gradient electrophoresis (NEPHGE), electroelution, Aqueous two phase partitioning

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