Proteomics
The term 'Proteomics' stands for systamatic analysis of protein profiles of tissues. Proteome refers to all proteins produced by a species, much as the genome is the entire set of genes.Proteomics is a branch of functional genomics that has arisen in response to the inevitable question posed by the genome sequencing projects, i.e., what are the functions of all the proteins? Proteomics can be
defined as the large-scale study of protein properties such as expression
levels, post-translational modifications and interactions with other molecules
to obtain a global view of cellular processes at the protein level. Because the
tools for high-throughput DNA and RNA analysis are not available for
protein analysis, the emphasis of functional genomics has been on the
mRNA message. However, it is the product of the mRNA, i.e., the protein,
which actually carries out the majority of the reactions of the cell. In addition, there is no a priori reason to expect that there will be a strict linear
relationship between mRNA levels and the protein complement or "proteome" of a cell. Proteomics is therefore a complementary approach to
genomics and mRNA expression mapping using microarrays. Finally, most
drug targets are proteins; therefore, methods to efficiently analyze the
protein complement of cells should contribute directly to drug development.
The activity most often associated with proteomics is fractionating and visualizing large numbers of proteins from cells on two-dimensional (2D) polyacrylamide gels. These types of experiments have been performed for more than twenty years to build databases of proteins expressed from certain cell or tissue types (Anderson and Anderson, 1996; O'Farrell, 1975).
Although this remains an important component of proteomics research, the field has expanded due to the development of additional technologies. Proteomics can be broadly divided into two areas of research: (i) protein expression mapping, and (ii) protein interaction mapping. Protein expression mapping involves the quantitative study of global changes in protein expression in cells, tissues or body fluids using 2D gel electrophoresis coupled with mass spectrometry. The identity of proteins within spots on 2D gels can be rapidly determined by in-gel proteolysis and peptide mass fingerprinting using mass spectrometry. In addition, recent developments in tandem mass spectrometry using nano-electrospray methods and enabled partial sequence information to be rapidly generated from spots on 2D gels. Thus, it is possible to generate databases of protein expression profiles for various cells and tissues (Rasmussen et al., 1996). In addition, rapid progress has been made in the identification of post- translational modifications of proteins (Oda et al., 2001; Zhou et al., 2001). This information is also being incorporated into protein expression profile databases. The aim of protein expression mapping is to compare the spectrum of proteins expressed in cells or tissues under different environmental conditions or from different disease states. Furthermore, an understanding of post-translational modifications of expressed proteins under different conditions or disease-states is sought. For clinical applications, the objective of protein expression mapping is to identify proteins that are up- or downregulated or modified in a disease-specific manner to use as diagnostic reagents or possible therapeutic targets. For basic research, the goal is to understand how the regulation of protein levels or modifications contributes to the execution and coordination of cellular processes.
The activity most often associated with proteomics is fractionating and visualizing large numbers of proteins from cells on two-dimensional (2D) polyacrylamide gels. These types of experiments have been performed for more than twenty years to build databases of proteins expressed from certain cell or tissue types (Anderson and Anderson, 1996; O'Farrell, 1975).
Although this remains an important component of proteomics research, the field has expanded due to the development of additional technologies. Proteomics can be broadly divided into two areas of research: (i) protein expression mapping, and (ii) protein interaction mapping. Protein expression mapping involves the quantitative study of global changes in protein expression in cells, tissues or body fluids using 2D gel electrophoresis coupled with mass spectrometry. The identity of proteins within spots on 2D gels can be rapidly determined by in-gel proteolysis and peptide mass fingerprinting using mass spectrometry. In addition, recent developments in tandem mass spectrometry using nano-electrospray methods and enabled partial sequence information to be rapidly generated from spots on 2D gels. Thus, it is possible to generate databases of protein expression profiles for various cells and tissues (Rasmussen et al., 1996). In addition, rapid progress has been made in the identification of post- translational modifications of proteins (Oda et al., 2001; Zhou et al., 2001). This information is also being incorporated into protein expression profile databases. The aim of protein expression mapping is to compare the spectrum of proteins expressed in cells or tissues under different environmental conditions or from different disease states. Furthermore, an understanding of post-translational modifications of expressed proteins under different conditions or disease-states is sought. For clinical applications, the objective of protein expression mapping is to identify proteins that are up- or downregulated or modified in a disease-specific manner to use as diagnostic reagents or possible therapeutic targets. For basic research, the goal is to understand how the regulation of protein levels or modifications contributes to the execution and coordination of cellular processes.