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Proteomics is the large-scale study of protein, particularly their structures and functions. This term was coined to make an analogy with genomics, and while it is often viewed as the "next step", proteomics is much more complicated than genomics. Most importantly, while the genome is a rather constant entity, the proteome differs from cell to cell and is constantly changing through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different parts of its body, in different stages of its life cycle and in different environmental conditions.
The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively.
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 completion of a rough draft of the human genome, many researchers are now 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 there are proteins in the human proteome (~20,000 to 25,000 genes vs. ~1,000,000 proteins). The large increase in protein diversity is thought to be due to alternative splicing and post-translational modification of proteins. This discrepancy implies that protein diversity cannot be fully characterized by gene expression analysis alone, making proteomics a useful tool for characterizing cells and tissues of interest.
To catalog all human proteins and ascertain their functions and interactions presents a daunting challenge for scientists. An international collaboration to achieve these goals is being co-ordinated by the Human Proteome Organisation (HUPO).
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Branches of proteomics
Protein separation. All proteomic technologies rely on the ability to separate a complex mixture so that individual proteins are more easily processed with other techniques.
Protein quantification. Gel-based methods are used, including differential staining of gels with fluorescent dyes (difference gel electrophoresis). Gel-free methods include various tagging or chemical modification methods, such as isotope-coded affinity tags (ICATs), metal coded affinity tags (MeCATs) or combined fractional diagonal chromatography (COFRADIC)*. In metabolic labeling cells incorporate heavy stable isotopes present in their growth media (e.g. stable isotope labeling with amino acids in cell culture or SILAC). Modern day gel electrophoresis research often leverages software-based image analysis tools primarily to analyze bio-markers by quantifying individual, as well as showing the separation between one or more protein "spots" on a scanned image of a 2-DE product. Additionally, these tools match spots between gels of similar samples to show, for example, proteomic differences between early and advanced stages of an illness.
Protein sequence analysis. This is more of a bioinformatic branch, dedicated to searching databases for possible protein or peptide matches, but also functional assignment of domains, prediction of function from sequence, and evolutionary relationships of proteins.
Protein modification. Almost all proteins are modified from their pure translated amino-acid sequence, so-called post-translational modification. Specialized methods have been developed to study phosporylation (phosphoproteomics) and glycosylation (glycoproteomics).
Cellular proteomics. A new branch of proteomics whose goal is to map the location of proteins and protein-protein interactions in whole cells during key cell events. Centers around the use of techniques such as X-ray Tomography and optical fluorescence microscopy.
Experimental bioinformatics. A branch of bioinformatics, as it is applied in proteomics, coined by Mathias Mann. It involves the mutual design of experimental and bioinformatics methods to create (extract) new types of information from proteomics experiments.
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Key technologies used in proteomics
Mass spectrometry (no-tandem), often MALDI-TOF, is used to identify proteins by peptide mass fingerprinting. This technology is also used in so-called "MALDI-TOF MS protein profiling" where samples (i.e. serum) are prepared by either protein chips (SELDI-TOF MS), magnetic beads (The Bruker Daltonics protein profiling platform) or with other methods of sample treatment, such as liquid chromatography, size-exclusion and immunoaffinity. Protein peaks of interest must be identified by tandem mass spectrometry. Protein profiling with MALDI-TOF MS could be of high use in clinical diagnostics, but so far there has been little succes with advancing MALDI-TOF MS protein profiling into clinical validation due to high analytical variation.
X-ray Tomography used to determine the location of labelled proteins or protein complexes in an intact cell. Frequently correlated with images of cells from light based microscopes.
Software based image analysis is utilized to automate the quantification and detection of spots within and among gels samples. While this technology is widely utilized, the intelligence has not been perfected yet. For example, the leading software tools in this area tend to agree on the analysis of well-definedm well-separated protein spots, but they deliver different results and tendencies with less-defined less-separated spots - thus necessitating manual verification of results.
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Protein databases
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See also
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