Proteome comparison

Li C, Zhan X, Li M, Wu X, Li F, Li J, et al. Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues. Genomics Proteomics Bioinformatics 2003 l(l) 58-67. 

Previous studies have used proteome comparisons to study such neurological disorders as Alzheimer s disease (AD), Parkinson s disease (PD), frontotemporal dementia, schizophrenia, and Creutzfeldt-Jacob disease. Some examples of utilizing proteomics approaches for discovery of biomarkers for neurological disorders in human CSF are given in Table 49.2. 

These recent studies have concluded that there is an inherent limitation of two-dimensional gels, namely that of maximum load compared to the range of protein abundances, which precludes low abundance protein identification. It would appear from these conclusions that, to be useful in detecting any protein with less than moderate abundance, 2DE must be applied to subfractionated or otherwise enriched samples, hi fact, the same groups have already started using and advocating mass spectrometry-based techniques for proteome comparison, bypassing completely the 2DE step. ... 

NegProt http //superfly.ucsd.edu/negprot Complete proteome comparison... 

Proteomics Study and comparison of the entire complement of proteins (proteome) under a given condition a cell s proteome, comparison of a normal liver proteome before and after drug treatment, comparison of proteomes from normal tissues with cancerous tissues. 

FEN 11] Feng M., Song F., Aleku D.W. et al., Antennal proteome comparison of sexually mature drone and forager honeybees . Journal of Proteome Research, vol. 10, pp. 3246-3260, 2011. 

In E. Coli bacterial lysates, the proteome (i.e., the full array of proteins produced) was analyzed by isoelectric focusing and mass spectrometry.97 A comparison of capillary electrophoretic separation and slab gel separation of a recombinant monoclonal antibody demonstrated that the precision, robustness, speed, and ease-of-use of CE were superior.98 Seventy-five proteins from the yeast ribosome were analyzed and identified by capillary electrophoresis coupled with MS/MS tandem mass spectrometry.99 Heavy-chain C-terminal variants of the anti-tumor necrosis factor antibody DE7 have been separated on capillary isoelectric focusing.100 Isoforms differing by about 0.1 pi units represented antibodies with 0,1 or 2 C-terminal lysines. 

Tammen, H., Schulte, I., Hess, R., Menzel, C., Kellmann, M., Mohring, T., Schulz-Knappe, P. (2005). Peptidomic analysis of human blood specimens comparison between plasma, specimens and serum by differential peptide display. Proteomics 5, 3414-3422. 

Essader, A.S., Cargile, B.J., Bundy, J.L., Stephenson, J.L., Jr. (2005). A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics. Proteomics 5, 24—34. 

A comparison of theoretical and practical peak capacity values, summarized in Table 12.2, leads to a conclusion that even the most promising 2DLC setups do not provide for the peak capacity needed to fully resolve a complex proteomic sample. As a result, the eluent entering the MS source typically contains multiple coeluting peptides. 

Bjorhall, K., Miliotis, T., Davidsson, P. (2005). Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 5, 307-317. 

Cole AR et al. Proteomic analysis of colonic crypts from normal, multiple intestinal neoplasia and p53-null mice a comparison with colonic polyps. Electrophoresis 2000 21 1772-1781. 

Betts JC et al. Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology 2000 146 3205-3216. 

TABLE 20.1 Summary of IHC Staining Results and Comparison with Spectral Counts Measured by Shotgun Proteomics... 

M. Yamada, M. Elias, K. Matsushita, C.T. Migita, and O. Adachi, Escherichia coli PQQ-containing quinoprotein glucose dehydrogenase its structure comparison with other quinoproteins. Biochim. Biophys. Acta Proteins Proteomics 1647, 185-192 (2003). 

The proteomics research of a number of scientists was described in a C E News report of the 2001 Pittcon meeting.10 One group, that of Catherine Fenselau at the University of Maryland, has studied a new method for proteolytic stable isotope labeling to provide quantitative and concurrent comparisons between individual proteins from two entire proteome pools.11 Two lsO atoms are incorporated into the... 

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