Proteomic approach

Nelson, R. W., Nedelkov, D., and Tubbs, K. A. (2000). Biosensor chip mass spectrometry A chip-based proteomics approach. Electrophoresis 21, 1155-1163. 

Warscheid, B. Fenselau, C. A targeted proteomics approach to the rapid identification of bacterial cell mixtures by MALDI mass spectrometry. Proteomics 2004, 4, 2877-2892. 

Hollyfield, JG, Salomon, RG, and Crabb, JW, 2003. Proteomic approaches to understanding age-related macular degeneration, In LaVail, MM, Anderson, RE, and Hollyfield, JG (Eds.), Retinal Degenerations Mechanisms and Experimental Therapy. Kluwer Academic/Plenum Publishers, New York, pp. 83-89. 

The combination of this top-down proteomics approach, which generates information on the structure of the intact protein, with a bottom-up approach for protein identification (using MS/MS data of tryptic peptides from the collected fractions) has been particularly useful for identifying posttranslational modifications, cotransla-tional processing, and proteolytic modifications in a number of proteins. Examples from our work will be shown to illustrate this hybrid methodology for proteomics analysis. 

Joubert-Caron R et al. Protein analysis by mass spectrometry and sequence database searching a proteomic approach to identify human lymphoblastoid cell line proteins. Electrophoresis 2000 21 2566— 2575. 

Dunn MJ Studying heart disease using the proteomic approach. DDT 2000 5 76-84. 

Pardo M et al. A proteomic approach for the study of Saccharomyces cerevisiae cell wall biogenesis. Electrophoresis 2000 21 3396-3410. 

Phan-Thanh L et al. A proteomic approach to study the acid response in Listeria monocytogenes. Electrophoresis 1999 20 2214-2224. 

Cheung W, Darfler M, Alvarez H, et al. Apphcation of a global proteomic approach to archival precursor lesions deleted in malignant brain tumors 1 and tissue transglutaminase 2 are upregulated in pancreatic cancers. Pancreatology 2008 8 608-616. 

Guerrero C, Tagwerker C, Kaiser P, et al. An integrated mass spectrometry-based proteomic approach quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics. 2006 5 366-378. 

Kraljevic Pavelic S, Sedic M, Hock K, et al. An integrated proteomics approach for studying the molecular pathogenesis of Dupuytren s disease. J. Pathol. 2009 217 524-533. 

Protein (as pure as possible) is specifically cleaved with a protease under defined conditions. Thus the mixture of peptides, specific for the given protein, is produced. In classical proteomic approach this step is generally preceded by separation of individual proteins, usually by two-dimensional electrophoresis. 

Chaudhuri, A.R., de Waal, E.M., Pierce, A., Van Remmen, H., Ward, W.F., and Richardson, A. (2007) Detection of protein carbonyls in aging liver tissue A fluorescence-based proteomic approach. Mech. Ageing Dev. 127(11), 849-861. 

Figure 4.4 The proteomics approach. Refer to text for details...

Graves, P. R. and Haystead, T. A., A functional proteomics approach to signal transduction, Recent. Prog. Horm. Res., 58, 2003. 

B. Warscheid and C. Fenslau. A Targeted Proteomics Approach to the Rapid Identification of Bacterial Cell Mixtures by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Proteomics, 4(2004) 2877-2892. 

Peng, J. et al. A proteomics approach to understanding protein ubiquitina-tion. Nat Biotechnol 2003, 21, 921—6. 

Ferro A, Olivera B (1982) Poly(ADP-ribosylation) in vitro. J Biol Chem 257 7808-7813 Gagne JP, Hunter JM, Labrecque B, Chabot B, Poirier GG (2003) A proteomic approach to the identification of heterogeneous nuclear ribonucleoproteins as a new family of poly(ADP-ribose)-binding proteins. Biochem J 371 331-340... 

Marcotte ER, Srivastava LK, Quirion R. 2003. cDNA microarray and proteomic approaches in the study of brain diseases focus on schizophrenia and Alzheimer s disease. Pharmacol Ther 100 63. 

Kanninen, K., Goldsteins, K., Goldsteins, G., Aiuiola, S., Alafuzoff, L, Koistinaho, J. (2004) Glycosylation changes in Alzheimer s disease as revealed by a proteomic approach. Neurosci. Lett., 367, 235-240. 

Y. G. Yeung and E. R. Stanley, Proteomic approaches to the analysis of early events in CSF-1 signal transduction. Mol. Cell. Proteomics2, 1143-1155 (2003). 

As we noted earlier, there are some very good reasons to consider proteomic approaches in drug discovery, for example ... 

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