Dynamic proteome

Recent developments in instrument design have led to lower limits of detection, while new ion activation techniques and improved understanding of gas-phase ion chemistry have enhanced the capabilities of tandem mass spectrometry for peptide and protein structure elucidation. Future developments must address the understanding of protein-protein interactions and the characterization of the dynamic proteome (Chalmers and Gaskell 2000). 

Peeieeer, K., Meyer, H. E., Eggert, A., Schramm, A. (2005a). Identification of dynamic proteome changes upon ligand activation of Trk-receptors using two-dimensional fluorescence difference gel electrophoresis and mass spectrometry. Mol. Cell Proteomics 4, 291-299. 

The focus in proteomics is still on protein discovery and protein structure analysis rather than on dynamic proteomics and protein function. 

Sigal, A.,Milo, R., Cohen, A., Geva-Zatorsky, N., Klein, Y.,Alaluf, I., Swerdlin, N., Perzov, N., Danon, T, Liron, Y, Raveh, T., Carpenter, A.E., Lahav, G. and Alon, U. (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat. Methods 3, 525-531. 

Dynamic Proteomics http //www.weizmann. ac.il/mcb/ UriAlon/DynamProt/ Dynamics of proteins in living human cells... 

Terentiev, A. A., Moldogazieva, N. T, Shaitan, K. V. The dynamic proteomics in the modeling of living cell. Protein-protein interactions. Success of biological chemistry (Advance in Biological Chemistry), 49,429-480,2009 (article in Russian). 

Cohen, A.A., Geva-Zatorsky, N., Eden, E. et al. 2008. Dynamic proteomics of individual cancer cells in response to a drug. Science 322 1511-1516. 

The proteome has been defined as the entire protein complement expressed by a genome. Thus the field of proteomics involves the extensive study of the dynamic protein products of the genome and includes... 

Chen, J., Gao, J., Lee, C.S. (2003b). Dynamic enhancements of sample loading and analyte concentration in capillary isoelectric focusing for proteome studies. J. Proteome Res. 2, 249-254. 

The enormous dynamic range of proteins in the sample represents an additional difficulty in proteome analysis. The best example is semm with a protein abundance ranging over eleven orders of magnitude (Anderson and Anderson, 2002). To detect the low abundant species, one has to load a sufficient amount of digest on a column to meet the limit of detection (LOD) of the MS instrument. Some reports published used up to 2.5 L of plasma with an extensive fractionation of intact proteins prior to LC-MS analysis on the peptide level (Rose et al., 2004). 

Fluorescein-5-maleimide also has been used to study the assembly dynamics of mycobacterium tuberculosis (Chen et al., 2007), to study monomers and dimers of nhaa Na+/H+ antiporter of E. coli (Rimon et al., 2007), and to investigate the regulation of the protein disulfide proteome by mitochondria (Yang et al., 2007). 

Figure 7.6. (a) Definitions of success rate and relative dynamic range, (b) Model of a proteomics experiment. (See color insert.)... 

The dynamic range of protein expression represents a main obstacle since abundant proteins are seldom of interest and others such as transcription factors are only present in a few copies. There is no detector that is able to visualize all proteins at the same time so that prefractionation and the investigation of subproteomes is required. In fact, pre-MS sample preparation techniques exploiting electrophoretic, chromatographic, or chemical properties of the analyte are often the bottleneck of proteomics. 

Mahmoud Hamdan and Pier Giorgio Righetti Proteomics Today Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology Igor A. Kaltashov and Stephen J. Eyles Mass Spectrometry in Biophysics Confirmation and Dynamics of Biomolecules... 

Nobuhiro Takahashi and Toshiaki Isobe Proteomic Biology Using LC-MS Large Scale Analysis of Cellular Dynamics and Function... 

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