Proteomic technologies for complex samples

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Biological processes in cells are intrinsically dynamic and this dynamicity can be affected by diseases and other factors. At the protein level, the dynamicity is manifested by changes in the amount of specific proteins and in the modifications that these proteins carry. Therefore, the ability to identify and monitor the level of proteins in the cell and the changes in their modification can greatly help our understanding of biological process and potentially provide new approaches for drug development. Unfortunately, techniques that are capable of following the ensemble of proteins present in cells (the proteome) are currently not available. In recent years, we and other groups have focused on breaking the proteome into parts called sub-proteomes. We have demonstrated that by studying sub-proteomes, proteins never observed before can be analyzed and that simple mass spectrometry based techniques can be used. We propose to develop a suite of stand-alone technologies, based on affinity purification and miniaturization that will allow the purification and processing of sub-proteomes. In particular, we will develop simple two and three dimensional miniaturized systems that combine microscale techniques to target specific sub-proteomes with microscale techniques and then process the proteins in that proteome. These stand-alone systems will be compatible with simple mass spectrometry techniques readily available in many laboratories. We propose to build systems for quantitating protein levels in sub-proteomes and to look at the changes in protein phosphorylations in these sub-proteomes. We envision that over time we will have an array of these sub-proteome analytical systems that can be commercialized and used to provide a better model and increased understanding of biological processes resulting in new approaches for drug development. This will be an important development for the field of proteomics because it will allow more proteins to be identified and quantified, and it will be readily adaptable in other research laboratories. The development of novel technologies is of great importance to Canada, especially those that can be commercialized and can have direct application for better understanding human diseases.