Multidimensional chromatography: An essential tool for proteomics

The general strategy in proteomic research consists in sample preparation, protein or peptide separation, their identification, and data interpretation. A critical step is certainly protein or peptide separation. Since increasingly complicated biological structures are studied by mass spectrometry (MS), the need for more powerful and highly resolving separation methods is growing. Consequently, multidimensional separation techniques in combination with MS have emerged as a powerful tool for the large-scale proteomic analysis. Until recently, two dimensional gel electrophoresis (2-DE) was the technique most often used for protein separation. The limitations of 2-DE in detecting low abundance, very small or large proteins, basic and membrane/ hydrophobic ones, as well as difficulties with process automation, have forced researchers to look for other methods of protein separation, such as multidimensional liquid chromatography coupled to MS (MDLC-MS) or LC to increase the peak capacity, and thus the resolving power of separation, to better fractionate peptides prior to entering the mass spectrometer. In this chapter, we analyze status and recent developments of the MDLC experiments in their fundamental components. It describes a variety of separation modes that have been employed to achieve protein-level or peptide-level separation, including size exclusion chromatography, ion exchange chromatography, and reversed-phase chromatography. We also discuss the advantages and disadvantages of two different approaches that can be followed for the studies of proteomics: protein-level separation or peptide-level separation. © 2011 by Nova Science Publishers, Inc. All Rights Reserved.