Other Proteomic Technologies

Despite the availability of rapid, convenient, and robust biomarker assays in these areas, considerable efforts are underway in the broadening arena of proteomics to develop new tools to serve the clinical market. Most developments have gone in the direction of miniaturization, taking advantage of the technological achievements of genomic platforms, for example, microarray spotting. Smaller apparatus means smaller sample quantities, and "lab-on-a-chip" technology suggests an ideal way to overcome the hurdle of sample size that limits conventional proteomics. Improvements in detection sensitivity through signal amplification and affinity capture, or a combination of both, have opened the way to true high-throughput proteomics requiring only tiny amounts of protein. Examples include random affinity capture of whole proteins, specific capture of proteins, and specific capture of peptides. SELDI (surface enhanced laser desorption ionization) generates mass spectra from samples of whole proteins, or trypsin-digested peptides, which are analyzed for statistically significant differences between diseased and normal samples (36,37). This technology has been coupled with laser capture microdissection (LCM), in which a few thousand diseased cells are separated from normal cells in order to produce a purified sample for comparison (38,39). LCM samples can also be applied to other miniaturized proteomic applications, such as those utilizing specific affinity capture. Other platforms have combined microfluidic technology, immobilization chemistries, and specific affinity reagents with high sensitivity optical or mass spectro-metric detection to produce affinity capture arrays on a microscopic scale (40). Scrivener et al. (41) have developed an affinity array detection system based on peptide affinity capture, which can be adapted to both fluorescence-based detection and full MS/MS analysis of peptide sequence. In a "reverse proteomics" approach, SEREX (serological analysis of recombinantly expressed clones), cDNA libraries are expressed in an array format, and their resulting recombinant proteins are reacted with sera from autologous patients (42,43). Antibodies or other serum proteins specific to disease state (to date, largely in cancer analyses, 44), identify their corresponding sets of antigens, which can define new diagnostic markers or therapeutic targets. The concept of recombinant protein arrays has been taken further by the Protein Expression group at the Max Planck Institute for Molecular Genetics (45), who propose to express 10,000 human proteins with the purpose of elucidating protein-protein, DNA-protein, and ligand-protein interactions and to profile and characterize antibody and sera-protein binding onto the array.

These new platforms have advantages over conventional 2D gel proteomics in terms of sample consumption—statistically significant analyses can be performed using quantities of protein that are orders of magnitude smaller. Their limitation lies in the number of proteins they can accurately identify. In the case of SELDI this may be inconsequential provided clear sets of markers can be identified independent of sample variation and noise. For protein "chips," specific affinity reagents need to be generated beforehand. Theoretically it would be possible to produce an affinity partner for almost every protein or peptide (a parallel to today's genomic microarrays), but in practice there is still a substantial lead time to manufacture such a comprehensive array. Nevertheless, as a research tool protein chips hold considerable promise.

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