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The Prospects and Challenges of Proteomics

Roland Annan

What is a Proteome & what is Proteomics?

The proteome has been defined as the protein content of a cell, a tissue or an entire organism in a defined state. Proteomics describes the global analysis of protein expression and function. On the one hand proteomics as a science is in its infancy. The technologies on which proteomics is currently based are singly or collectively, immature, complex, labor intensive and fraught with difficulty. On the other hand, the prospects of the knowledge to be gained on how living things work, makes proteomics with all its challenges, worth doing. The realization that the human genome contains only approximately 30,000 genes, one third more than a fruit fly, suggests the future belongs to proteomics. Clearly these 30,000 genes must be multi tasking in order for so few of them to produce and operate an exquisitely complex machine like the human body. Thus our understanding of cellular systems will depend on our ability to identify proteins and quantitate their expression levels, determine their modification states, localizations, interaction partners and assign their functions. These may be different for each type of cell and change dramatically at different points in the cell cycle or according to various types of cellular stimulation or perturbation. The challenge is formidable.

Proteomics: A New Challenge for Separation Science

William S. Hancock

New developments in biotechnology products will be centered on the treatment of more complex diseases and the growing requirement for patient specificity. This trend is encapsulated in terms such as Predictive or Personalized Medicine. The appropriate technological developments to respond to these challenges must be based on global studies of biological systems. With the advent of sequencing of a variety of genomes and initial developments in proteomics we are beginning to have the tools necessary for such global studies. This lecture will concentrate on recent developments in proteomics as an example of such studies. As a definition, proteomics refers to the global characterization of the full set of proteins present in a biological sample. Also higher-order information may be required, such as localization and protein-protein interactions. Improved high efficiency and selectivity separations will have a major contribution to the characterization of the proteome. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity will be required in disease studies. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. As has been discovered with the combination of MALDI-TOF and 2D gel proteomics studies, the measurement of low abundance proteins is compromised by the inability to achieve good ionization of complex peptide and protein mixtures. Therefore, highly efficient separation processes are an absolute requirement for advanced proteomic studies.

Peptide mapping with multidimensional HPLC-ion trap mass spectrometry (MS/MS) procedures can allow the characterization of at least 200 proteins per hour. Another advantage of such an approach is the ability to define post-translational modifications such as glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components.

Future developments in the field of proteomics will require the development of a new set of high-throughput tools for the fractionation of biological samples that allow the preparation of protein fractions suitable for the MS/MS approach. This step will allow the characterization of the complex sets of protein mixtures present in different cellular regions. This presentation will show how proteomic approaches can be of relevance to the production of new protein pharmaceuticals as demonstrated by the characterization of novel glycoproteins and other complex biological samples.

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