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Robotic preparation of MALDI mass spectrometry samples on a sample carrier.

Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital in living organisms, as they are the main components of the physiological pathways of cells. The term "proteomics" was coined to make an analogy with genomics, the study of the genes. The proteome of an organism is the set of proteins produced by it during its life, and its genome is its set of genes. The proteome of a cell under a particular stimulation is the set of proteins in it. The word "proteome" derives from "proteins" and "genome", since proteins are expressed by the genome.

Proteomics is often considered the next step in the study of biological systems, after genomics. It is much more complicated than genomics, mostly because while an organism's genome is rather constant, a proteome differs from cell to cell and constantly changes through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different parts of its body, different stages of its life cycle and different environmental conditions. Another major difficulty is the complexity of proteins relative to nucleic acids.

Scientists are very interested in proteomics because it gives a much better understanding of an organism than genomics. First, the level of transcription of a gene gives only a rough estimate of its level of expression into a protein. An mRNA produced in abundance may be degraded rapidly or translated inefficiently, resulting in a small amount of protein. Second, many proteins experience post-translational modifications that profoundly affect their activities; for example some proteins are not active until they become phosphorylated. Methods such as phosphoproteomics and glycoproteomics are used to study post-translational modifications. Third, many transcripts give rise to more than one protein, through alternative splicing or alternative post-translational modifications. Finally, many proteins form complexes with other proteins or RNA molecules, and only function in the presence of these other molecules.

Since proteins play a central role in the life of an organism, proteomics is instrumental in discovery of biomarkers, such as markers that indicate a particular disease.

With the completion of a rough draft of the human genome, many researchers are looking at how genes and proteins interact to form other proteins. A surprising finding of the Human Genome Project is that there are far fewer protein-coding genes in the human genome than proteins in the human proteome (20,000 to 25,000 genes vs. about 1,000,000 proteins). The human body may contain more than 2 million proteins, each having different functions. The protein diversity is thought to be due to alternative splicing and post-translational modification of proteins. The discrepancy implies that protein diversity cannot be fully characterized by gene expression analysis, thus proteomics is useful for characterizing cells and tissues.

To catalog all human proteins, their functions and interactions is a great challenge for scientists. An international collaboration with these goals is co-ordinated by the Human Proteome Organization.

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