High proteome profiling

Wang, H., Clouthier, S.G., Galchev, V., Misek, D.E., Duffner, U., Min, C.K., Zhao, R., Tra, J., Omenn, G.S., Ferrara, J.L., Hanash, S.M. (2005). Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol. Cell. Proteomics 4, 618-625. 

Lopez MF et al. High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation. Electrophoresis 2000 21 3427-3440. Reinheckel T et al. Adaptation of protein carbonyl detection to the requirements of proteome analysis demonstrated for hypoxia/reoxygenation in isolated rat liver mitochondria. Arch Biochem Biophys 2000 376 59-65. 

Nishizuka, S., Charboneau, L., Young, L., Major, S., Reinhold, W.C., Waltham, M., Kouros-Mehr, H., Bussey, K.J., Lee, J.K., Espina, V., Munson, RJ., Petricoin, E., Liotta, L.A., and Weinstein, J.N., Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays, Proc. Natl. Acad. Sci. USA, 24, 14229-14234, 2003. 

Madera, M., Mechref, Y, Klouckova, I., and Novotny, M. V., Semiautomated high-sensitivity profiling of human blood serum glycoproteins through lectin preconcentration and multidimensional chromatography/tandem mass spectrometry. Journal of Proteome Research 5(9), 2348-2363, 2006. 

Aldor IS, Krawitz DC, Forrest W et al (2005) Proteomic profiling of recombinant Escherichia coli in high-cell-density fermentations for improved production of an antibody fragment biopharmaceutical. Appl Environ Microbiol 71 1717-1728... 

This approaeh was suggested and adopted by two groups of researehers (Steel et ah, 2001 Poon and Johnson, 2001). However, one of the problems of this method is due to the presence of a few highly abundant proteins such as albumin, transferrin, and immunoglobulin G (IgG) in the serum proteome profile, which may distort the separation and/or mask the minor proteins present. Thus selective removal of these proteins, especially albumin (representing 30-50% of the total serum protein) is recommended prior to Ifactionation by 2-DE. In many cases, the differences in the protein of interest in the serum protein profile may be due to post-translational modifications, especially glycosylation. In fact, different glycosylated forms of AFP were detected in the sera of HCC patients (Johnson et ah, 1999). 

Table 3.2 summarizes the most popular proteome profiling techniques. Recent developments introduced capillary electrophoresis [92] not only for DNA analysis and sequencing, but also for high-resolution protein separation, based on their size (capillary electrophoresis-sodium dodecyl sulfate [CE-SDS]) and capillary isoelectric focusing (cIEF) point... 

In order to evaluate the proteomic profile of whole cells and to correctly identify proteins based solely on the intact mass, advanced instrumentation offering high mass accuracy is necessary. The application of Fourier transform mass spectrometry (FTMS) to intact cell analysis allowed for unambiguous identification of biomarker proteins due to the high resolution and mass... 

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