Profiling proteome analysis

Figure 11.2 Overview of ChemProteoBase profiling. Proteomic analysis is performed by 2D-DIGE, and expression data of around 300 spots are acquired. Compared with data sets of well-characterized compounds in ChemProteoBase, the plausible target is predicted by finding the most similar compounds in proteomic profile. On the basis of the prediction, validation studies are performed.

Lopez MF et al. High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation. Electrophoresis 2000 21 3427-3440. Reinheckel T et al. Adaptation of protein carbonyl detection to the requirements of proteome analysis demonstrated for hypoxia/reoxygenation in isolated rat liver mitochondria. Arch Biochem Biophys 2000 376 59-65. 

T., Kamo, M., Matsui, T., Watanabe, Y., Mori-masa, T., Hosokawa, K., Toda, T. (2000) Proteome analysis of mouse brain two-dimensional electrophoresis profiles of tissue proteins during the course of aging. Electrophoresis. 21,1853-1871... 

The reproducible high-resolution separation of protein mixtures is the main purpose of proteome analysis. O FarelTs classic tube gel technique has limited reproducibility. It is often difficult to compare the protein profiles obtained using O FarelTs method in different laboratories. In some cases, the data obtained even in the same laboratory by different operators are not comparable. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

To address this problem, recently a new strategy for proteome analysis has emerged. This technology, named Combinatorial Proteomic, uses antibody libraries as probes to profile the expression and function of protein families in complex proteomes. The use of antibodies allows the detection of iper- and ipo-expressed proteins, even if they are at pico-quantity level, overcoming one of the proteomic limitations of difficulty in detecting low abundance proteins [46, 47],... 

Figure 4.3. Fields of proteomic research. Proteomic research can be classified into six general research fields. Proteomic mapping and proteomic profiling constitute the first tier of proteomic analysis based upon identification and quantitation of proteins within a defined space of interest that can range from the entire organism to the protein level. The second tier of proteomic analyses is shown below involving global characterization of structure, function, posttranslational modifications, and association with other proteins (or other biochemical components).

The top tier of proteomic analysis categories—proteomic mapping and proteomic profiling—will continue to dominate the field of proteomics because investigators are interested in what proteins are present in their sample and how much. How much is typically a proportion of experimental treatment to control, but proteomic technologies are improving on their abilities to provide amounts and concentrations. Therefore, an important consideration in proteomic analysis is a realistic sense of how much of the proteome can actually be measured with the proteomic platform available in order to best answer the scientific problem at hand. 

The synovial proteome analysis of fibroblast-like synoviocytes. Arthritis Res. Ther. 6, R161-R168, 2004 Romeo, M.J., Espina, V., Lowenthal, M. et al., CSE proteome a protein repository for potential biomarker idenfi-cation. Expert. Rev. Proteomics 2, 57-70, 2005 Hueber, W., Kidd, B.A., Tomooka, B.H. et al.. Antigen microarray profiling of autoantibodies in rheumatoid arthritis. Arthritis Rheum. 52, 2645-2655, 2005. 

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