Highlights on the capacities of "Gel-based" proteomics

Proteomics, one of the most important areas of research in the post-genomic era, is not new in terms of its experimental foundations [1]. It is a natural consequence of the huge advances in genome sequencing, bioinformatics and the development of robust, sensitive, reliable and reproducible analytical techniques [2-12]. Genomics projects have produced a large number of DNA sequences from a wide range of organisms, including humans and mammals. This "genomics revolution" has changed the concept of the comprehensive analysis of biological processes and systems. It is now hypothesized that biological processes and systems can be described based on the comparison of global, quantitative gene expression patterns from cells or tissues representing different states. The discovery of posttranscriptional mechanisms that control rate of synthesis and half-life of proteins and the ensuing nonpredictive correlation between mRNA and protein levels expressed by a particular gene indicate that direct measurement of protein expression also is essential for the analysis of biological processes and systems. Global analysis of gene expression at the protein level is now also termed proteomics. The standard method for quantitative proteome analysis combines protein separation by high resolution (isoelectric focusing/SDS-PAGE) two-dimensional gel electrophoresis (2DE) with mass spectrometric (MS) or tandem MS (MS/MS) identification of selected protein spots [5,9,11,13-16]. Important technical advances related to 2DE and protein MS have increased sensitivity, reproducibility, and throughput of proteome analysis while creating an integrated technology. Quantitation of protein expression in a proteome provides the first clue into how the cell responds to changes in its surrounding environments. The resulting over- or under-expressed proteins are deemed to play important roles in the precise regulation of cellular activities that are directly related to a given exogenous stimulus. Conventio