Protein expression analysis

As well as protein expression analysis, proteomics in its broadest sense also includes protein-protein interaction mapping. This can range from small studies using a single protein or peptide to fish ouf any proteins that interact with it... 

Figure 6.15 Applying dual-color ratiometric gene expression labeling approach to protein expression analysis. (From Haab, B.B. etal., Genome Biol., 2, 0004.1-0004.13, 2001. With permission.)...

A fully automated two-dimensional electrophoresis (2DE) system for rapid and reproducible protein analysis is described. 2DE that is a combination of isoelectric focusing (lEE) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is widely used for protein expression analysis. Here, all the operations are achieved in a shorter time and all the transferring procedures are performed automatically. The system completed the entire process within 1.5 h. A device configuration, operational procedure, and data analysis are described using this system. 

Two-dimensional electrophoresis (2DE) that is a combination of isoelectric focusing (lEF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (4) is widely used for protein expression analysis. 

Kennedy S (2002) The role of proteomics in toxicology identification of biomarkers of toxicity by protein expression analysis. Biomarkers 7 269-290 Li J, Zhang Z, Rosenzweig J, Wang YY, Chan DW (2002) Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clinical Chemistry 48 1296-1304... 

For the investigation of expression changes due to xenobiotic/toxin exposure, proteins have to be extracted from samples of body fluids, tissues or cells. For this purpose, many protein extraction protocols have been developed and adapted to different sample types (Link 1999). All protocols follow the main objective to recover as much of the proteome as possible with as little contamination by other biomaterials as possible. Sample preparation has to be performed prior to any proteomics technology used in investigative studies, or predictive toxicology. Depending on the method used for protein expression analysis, fractionation steps have to follow or have to be implemented in the extraction procedures (Wilkins et al. 1997 Rabilloud 2000 Liebler 2002). 

Knowledge of protein primary sequence, quantities, posttranslational modifications (PTMs), structures, protein-protein (P-P) interactions, cellular spatial relationships, and functions are seven important attributes (see Table 4.2) needed for comprehensive protein expression analysis. It is this multifold and complex nature of protein attributes that has spawned the development of so different many proteomic technologies. Some of these challenges in proteomic analysis include defining the identities and quantities of an entire proteome in a particular spatial location (i.e., serum, liver mitochondria, brain), the existence of multiple protein forms and complexes, the evolving structural and functional annotations of the human and rodent... 

Figure 4.13. Summary of advantages and limitations of representative proteomic platforms for protein expression analysis. The capabilities and advantages (solid line) are compared to the drawbacks (dotted lines) for each proteomic platform. Explanation of advantages and limitations are briefly highlighted here and more thoroughly discussed in the text. Abbreviations for each platform are provided in the Figure 4.1 legend and in the text. Other abbreviations used are PTMs, posttranslational modifications ID, identification.

Hoffmann C, Schmitt K, Brandenburg A, Hartmann S (2007) Rapid protein expression analysis with an interferometric biosensor for monitoring protein production. Anal Bioanal Chem 387 1921-1932... 

Kennedy S (2002) The role of proteomics in toxicology Identification of biomarkers of toxicity by protein expression analysis. Biomarkers 7(4) 269-290. 

Man WJ, White IR, Bryant D, Bugelski P, Camilleri P, Cutler P, Heald G, Lord PG, Wood J, Kramer K. Protein expression analysis of drug-mediated hepatotox-icity in the Sprague-Dawley rat. Proteomics 2002 2(ll) 1577-85. 

Washurn, M.P. Koller, A. Oshiro, G. Ulaszek, R.R. Plouffe, D. Deciu, C. Winzeler, E. Yates, YR. Protein Pathway and Complex Clustering of Correlated inRNA and Protein Expression Analysis in Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 100, 3107-3112 (2003). 

Microfluidic devices that will enable global proteomic profiling will be particularly useful for biomarker discovery applications where the researcher is interested in comprehensively mapping all peptide/protein components in given biological fluids or tissues. Differential protein expression analysis will enable the discovery of specific protein markers or protein co-expression patterns that... 

Kopf, E., Shnitzer, D., Zharhary, D. (2005). Panorama Ab Microarray Cell Signaling kit a unique tool for protein expression analysis. Proteomics, 5, 2412-2416. 

Yamamoto, T., T. Eukushima, R. Kikkawa, H. Yamada, and 1. Horri. 2005. Protein expression analysis of rat testes Induced testicular toxicity with several reproductive toxicants. Journal of Toxicological Sciences 30 111-126. 

James P (2001). Protein expression analysis From tip of the iceberg to a global method. Disease Markers. 17 235-246. 

Man, W.J., White, I.R., Bryand, D., Bugelski, P., Kamilleri, P., et al., 2002, Protein expression analysis of drug-medicated hepatotoxicity in the Sprague-Dawley rat. Proteomics 2 1577-1585. 

Drummelsmith J, Girard I, Trudel N et al. Difierential protein expression analysis c Leishmania major reveals novel roles for methionine adenosyltransferase and S-adenosylmethionine in methotrexate resistance. J Bioi Chem 2004 279(32) 33273-80. 

Clarke, C., Henry, M., Doolan, P., Kelly, S. et al (2012) Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate. BMC Genomics, 13, 656. 

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