Principles of Proteomics

Proteomics is the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). The proteome is not constant; it differs from cell tofficell and changes over time. However, protein activity (often assessed by the reaction rate of the processes in which the protein is involved) is also modulated by many factors in addition to the expression level of the relevant gene. Several high-throughput technologies have been developed to investigate proteomes in depth. The most commonly applied are mass spectrometry (MS)-based techniques such as Tandem-MS and gel-based techniques such as differential in-gel electrophoresis (DIGE). These high-throughput technologies generate huge amounts of data. Databases are critical for recording and carefully storing this data, allowing the researcher to make connections between their results and existing knowledge. Proteomics is a rapidly growing field of molecular biology that is concerned with the systematic, high-throughput approach to protein expression analysis of a cell or an organism. Typical results of proteomics studies are inventories of the protein content of differentially expressed proteins across multiple conditions. Post-translational modifications, alternative splice products, and proteins intractable to classic separation techniques have presented a challenge towards the realization of the conventional definition of the word. Today, many different areas of study are explored by proteomics. Amongst them are protein-protein interaction studies, protein function, protein modifications, and protein localization studies. The fundamental goal of proteomics is not only to pinpoint all the proteins in a cell, but also to generate a complete three-dimensional map of the cell indicating their exact location. In many ways, proteomics runs parallel to genomics. The starting point for genomics is a gene in order to make inferences about its products (i.e. proteins), whereas proteomics begins with the functionally modified protein and works back to the gene responsible for its production. The techniques for proteome analysis are not as straightforward as those used in transcriptomics. However, the advantage of proteomics is that the real functional molecules of the cell are being studied. Strong gene expression, resulting in an abundant mRNA, does not necessarily mean that the corresponding protein is also abundant or indeed active in the cell. This Text is intended to give the molecular biologist a rudimentary understanding of the technologies behind proteomics and their application to address biological questions.