Proteome analysis differential protein targeting

In a more modified approach, differential display proteomics can also be done with no separation of proteins. This is called the protein chip approach. In this method, a variety of bait proteins such as antibodies, peptides, or protein fragments may be immobilized in an array format on specially treated surfaces. The surface is then probed with the samples of interest. Proteins that bind to the relevant target can then be analyzed by direct MALDI readout of the bound material (Nelson, 1997 Davies et ah, 1999). Lor example, well-characterized antibodies can be used as bait. Protein samples from two different cell states are then labeled by different fluorophores, mixed together, and used as probe. In such a case, the fluorescent color acts as an indicator for any change in the abundance of the protein that remains bound to the chip (Lueking et ah, 1999). A number of technical problems would still need to be overcome before applying this technique for large-scale analysis of proteins. 

Proteome analysis of HCC is an emerging area of research in the discoveiy of novel proteins as early biomarkers for diagnosis and potential therapeutic targets for the treatment of HCC. Although numerous publications have appeared on the gene expression analysis of HCC by cDNA microarrays, there is still a need to analyze the differentially... 

Quantitative proteomics is performed to determine the differential expression of proteins in two samples. This analysis, as an example, can provide comparative information of the proteomes of diseased and healthy subjects as a guide to biomarker discovery and to identify potential drug targets. A majority of the methods discussed in this chapter rely on isotopic labeling of the two samples in question with light and heavy isotopes and comparing the MS response. 

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