Proteomics expression

Pan, Y., Kislinger, T., Gramolini, A.O., Zvaritch, E., Kranias, E.G., MacLennan, D.H., Emih, A. (2004). Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics. Proc. Natl. Acad. Sci. USA 101, 2241-2246. 

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D.B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386. 

Moseley, M. A., Current trends in differential expression proteomics isotopically coded tags, Trends Biotechnol., 19 (10 Suppl), S10, 2001. 

Many proteomic studies have identified diverse proteins that may be involved in the pathogenic mechanism of disease and which may be disease markers. Most of the applications use expression proteomics to determine expression profiles of proteins in cells and tissues in normal or disease states. In the present study, we analyzed protein expression in cancer tissue samples and corresponding non-cancerous tissue samples to find proteins that might be involved in carcinogenesis or pathogenesis. 

Cell map proteomics reveals the static proteome of a whole organism, tissue, cell or organelle, while expression proteomics investigates changes in a proteome to cellular cues (Godovac-Zimmermann and Brown, 2001). Functional and structural proteomics refers to the investigation of individual proteins such as interactions with ligands. 

Among several different descriptions of the nature and purpose of proteomics, one of the most useful is the separation into expression proteomics and cell-map proteomics (Blackstock. 1999) ... 

A number of transgenic plants have been submitted to proteome analysis. For instance, in rice, Wang et al. (74) used classical two-dimensional electrophoresis and mass spectrometry to evidence that more than 50 proteins were differently expressed. Proteomics studies have been performed also in transgenic tomato (75), potato (76), and wheat (77) again by using standard analytical methods. 

General consensus has sub-divided proteomics into three main areas, Expression Proteomics, Functional Proteomics, and Structural Proteomics. Expression Proteomics (sometimes called differential-expression proteomics) involves the analysis of differential protein expression by protein... 

In contrast, Functional Proteomics concerns the manner in which proteins interact and, in turn, how these interactions determine function, both normal and abnormal. This approach is less reductionist than Expression Proteomics as proteins are studied in the context of their complex cellular interactions. Finally, Structural Proteomics is concerned with the primary through tertiary structure of proteins, and modifications therein, largely determined by x-ray and NMR analysis of protein crystals (20). In this chapter we will concern ourselves only with Expression and Functional Proteomics. 

As mentioned earlier, Functional Proteomics is concern with the manner in which proteins interact and, in turn, how these interactions ultimately determine function and dysfunction. This approach is less reductionist than Expression Proteomics because proteins are studied in the context of their complex cellular interactions. 

Over recent years, oncology has been a key focus of proteomic technologies as applied in both expression and functional studies. Expression proteomic studies are screening for differences in protein patterns between tumor and control tissues. Functional proteomic studies are defined as the combination of readouts with proteomics data from the same sample at different points of time (under different conditions), with the aim of detecting and prioritizing certain proteins or polypeptides of functional relevance. 

As of today, expression proteomic studies are available for all common human cancers and some rare tumors. 

Pandey, A., Mann, M. (2002). Stable isotope labeling by amino adds in cell culture, SI LAC, as a simple and accurate approach to expression proteomics. 

Classical Proteomic analysis based on the direct analysis of the expressed proteome... 

Due to the limitations of prediction, there is a need for projects that will collect data on subcellular location for a variety of conditions. These projects determine protein location rather than predict it. Although these projects are useful in their own right, they also serve as a way to expand the database for the prediction of protein location. One powerful approach to determination is to isolate specific organelles or stmctures and then identify their components by expression proteomics methods (Bmnet et al. 2003). This provides information rapidly for large numbers of proteins but has limited ability to distinguish different domains within an organelle. This chapter will focus on a complementary approach, automated determination of subcellular location using fluorescence microscopy. 

Binding of a Phi e-Expressed Proteome Library to a Small Molecule... 

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