Proteomics clinical

Today, most data are entered into corporate databases which consider the need of the user and the purpose of data. They are structured, searchable, contain both raw and metadata. Decision-making tools can mine these databases and if necessary combine data from various sources, including genetic, proteomic, clinical and chemical databases. 

Harada T, Kuramitsu Y, Makino A et al. Expression of tropomyosin alpha-4 chain is increased in esophageal squamous eell eareinoma as evideneed by proteomie profiling by two-dimensional electrophoresis and liquid ehromatography-mass speetrometry/mass spectrometry. Proteomics Clinical Applications 2007 1 215-223. 

When introduced the word proteomics was used to describe the ambitious goal of cataloging the proteins in different organisms. Today there are many more meanings and the field of proteomics has been differentiated considerably, with subdivisions such for, structural proteomics, clinical proteomics, and so forth. 

It is interesting to note that the foremost challenges for the detailed modeling of the intact organism (computing time, complexity of interactions, model selection) are very similar to those entailed by the analysis of proteomic or genomic data. In the clinical case, complexity shifts from the richness of the data set to the model formulation, whereas in the proteomic-genomic case the main source of difficulties is the sheer size of the data set however, at least at present, interpretative tools are rather uncomplicated. 

McKusick VA The anatomy of the human genome a neo-Vesalian basis for medicine in the 21st century. JAMA 2001 286 2289. (The November 14, 2001, issue contains a number of other excellent articles—eg, on clinical proteomics, pharmacogenomics—relating to the Human Genome Project and its impact on medicine.)... 

Voss Tet al. Correlation of clinical data with proteomics profiles in 24 patients with B-cell chronic lymphocytic leukemia. Int J Cancer 2001 91 180-186. 

Betts JC et al. Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology 2000 146 3205-3216. 

Many diseases are characterized by the expression of specific proteins1 in some cases, malignant cells yield unique protein profiles when total cellular protein extracts are analyzed by proteomic methods such as two-dimensional gel electrophoresis or matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS).2 High-throughput proteomic studies may be useful to differentiate normal cells from cancer cells, to identify and define the use of biomarkers for specific cancers, and to characterize the clinical course of disease. Proteomics can also be used to isolate and characterize potential drug targets and to evaluate the efficacy of treatments. 

When fresh or frozen tissue is used for proteomic analyses, the results cannot be related directly to the clinical course of diseases in a timely manner. Instead, researchers frequently reduce the number of interesting proteins to a manageable number and then attempt to use immunohistochemistry to understand the implications of proteomic changes in archival formalin-fixed, paraffin-embedded (FFPE) tissue for which the clinical course has been established.3 Unfortunately, immunohistochemistry is a semiquantitative pro-teomic method, and the choice of interesting proteins must occur without advance knowledge of the clinical course of the disease or the response to therapy. If routinely fixed and embedded archival tissues could be used for standard proteomic methods such as 2-D gel electrophoresis and mass spectrometry (MS), these powerful techniques could be used to both qualitatively and quantitatively analyze large numbers of tissues for which the clinical course has been established. However, analysis of archival FFPE tissues by... 

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