The current proposal will help to expand the Institute for System Biology's (ISB) Proteomics facility by providing capital to purchase a Fourier transform-ion cyclotron-resonance mass spectrometer (FTMS). Currently, the Proteomics facility focus is on large scale application of a novel approach to the systematic identification and accurate quantitation of the proteins present in cells and tissues and therefore detection of dynamic changes in global protein expression profiles that are characteristic for biological processes or medical conditions. Numerous collaborations exist between the facility and NIH supported biomedical researchers that are outlined in this proposal covering areas as diverse as interferon resistance to hepatitis C, androgen dependence in prostate cancer, stem cell biology, identification of proteins associated with Tollike receptors, functional analysis of the Myc oncoprotein, cell-cycle regulation of gene expression in the yeast Saccharomyces cerevisiae, thymocyte biology, and analysis of the proteins associated with the T-ceIl regulatory protein LAT and associated phosphorylation events. In addition to these NIH supported projects another 12 collaborations are ongoing between the facility with collaborators inside and out of the ISB. The availability of FTMS instrumentation in the facility will allow more thorough characterization of individual proteins and their post-translational modifications (PTM) and whole proteomes for each of these projects than is possible with any of the other types of mass spectrometers present in the greater Seattle area. The unique features of non-destructive ion detection by FTMS instrumentation provide exceptional performance in three critical mass spectrometric parameters that will benefit our biomedical research: 1) mass accuracy of 0.1 -1.0 ppm at 1000 u allow higher confidence in identifications of proteins from peptides by, for instance, the mass fingerprint approach, 2) mass resolution of >1 00,000 (50% mIDm) at 1000 u provides extraordinary capability in the area of complex mixture characterization where as many as 3000 components have been detected in a crude oil mixture (REF Marshall) and 3) signal-to-noise enhancement allows detection and fragmentation of peptides in the low attomole regime (Marshall). Data from an FTMS instrument in each of these three areas far exceeds the same capability from any other mass spectrometer that is currently available. Furthermore there are no FTMS instruments in the greater Seattle area for us, or our collaborators, to use.
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