To enhance the productivity of NIH-funded proteomics research of Chicago-area researchers, we propose to trade in an existing ion trap mass spectrometer (Thermo LCQ Deca) for a Thermo LTQ Orbitrap Velos high resolution mass spectrometer. This instrument will be located in the Chicago Biomedical Consortium/ University of Illinois at Chicago Research Resource Center Proteomics and Informatics Services Facility which serves researchers at Northwestern University, the University of Chicago, Argonne National Laboratory, and the University of Illinois at Chicago. Upgrading the system has the economic advantage of utilizing an existing Dionex 2D microcapillary HPLC system and laboratory space designed specifically for mass spectrometry. A unique aspect of our application is that we have engineered an Agilent Chip Cube microcapillary LC-nanoelectrospray system to operate on the LTQ Orbitrap Velos. We have demonstrated this capability by operating our modified Chip Cube on an LTQ Orbitrap Velos at the Thermo demonstration laboratory in California. The Chip Cube enables faster and more reproducible and reliable microcapillary HPLC separations and nanoelectrospray on the LTQ Orbitrap Velos than would otherwise be possible. To the best of our knowledge, no other laboratory has this capability. Our facility is the center of proteomics activity in the Chicago metropolitan area and is subsidized by the Chicago Biomedical Consortium to facilitate intercampus collaborative research between biomedical investigators. During 2009, our mass spectrometry laboratory carried out almost 11,000 hours of mass spectrometric analyses (not counting maintenance time), and almost 4,000 hours were devoted to proteomics using LC- MS/MS on a linear ion trap mass spectrometer and our FTMS. We have a user base of 245 proteomics investigators. The proposed LTQ Orbitrap Velos mass spectrometer is a high resolving power, high mass accuracy instrument that will enhance the efficiency and productivity of LC-MS/MS based proteomics such as protein identification and applications involving stable isotope labeled protein and peptides. Some of the applications that will benefit include quantitative studies of protein expression using iTRAQ, ICAT and SILAC and H/D exchange measurements of protein structure and function. These measurements are not currently practical in our facility due to slow scan speeds or sensitivity limitations on the FTMS or poor sensitivity at low mass and low resolution on the ion trap. The use of the Chip Cube technology will enhance throughput by reducing run times and increasing nanolectrospray reliability, and the high resolution of the Orbitrap Velos will enhance informatics throughput. Staffed with five Ph.D. level experts in mass spectrometry, proteomics and informatics, our facility is a major regional resource for proteomics research and education, and the proposed mass spectrometer will enhance the research productivity of all of our NIH-funded investigators.
