Proteomic Technologies for Complex Samples

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Proteins play essential roles in biological processes. These roles are reflected through changes in levels, interactions, localization and post-translational modifications of proteins. Therefore, the ability to identify and monitor the level of proteins in the cell and the changes in their modifications can greatly help our understanding of biological processes. Technologies are being developed to study the proteome (ensembles of proteins). Unfortunately, these technologies are not able to look at all the proteins. This leads to under-representation of important subgroups of proteins in proteomic studies. In particular, plasma membrane proteins which are important for drug discovery, cell signaling, and other biological processes are often under-represented using current proteomic technologies. More importantly, even when they are observed by global proteomic technologies, the information about the changes in protein levels and modifications that are specific to the membrane can be overshadowed. We propose to develop microfluidic technologies that will allow the study of sub-proteomes based on cellular compartments with an initial focus on plasma membrane proteins. Our short term objectives (1-3 years) are to develop new membrane solubilization protocols and an ensemble of microfluidic technologies for processing, identifying and relative quantitating membrane proteomes by mass spectrometry. An important aspect of our objectives is to provide training for students, postdoctoral fellows, and visiting scientists on the development of microfluidic proteomic technologies and mass spectrometry. Our medium term objectives (3-5 years) are to integrate these technologies into single devices to demonstrate their compatibility for analyzing sub-proteomes. Our long term objective is to apply these microfluidic technologies to study the dynamicity of the membrane proteome, to automate these systems, and to explore their commercialization.