Acquisition of OrbiTrap Eclipse w/FAIMS mass spectrometer

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Project Summary/Abstract: This application is for funds to purchase a Thermo Scientific Orbitrap Eclipse w/FAIMS mass spectrometry system for Fred Hutchinson Cancer Research Center’s Proteomics Facility. The facility supports the Fred Hutchinson/University of Washington Cancer Consortium which is made up of these two institutions and research partners at Seattle Children’s Research Institute and the Seattle Cancer Care Alliance and has a combined annual NIH grant base exceeding $300 million. Our facility has been operating for 20 years and we have a combined 75+ years’ experience in the operation, maintenance, and management of mass spectrometry instrumentation, and in the design and analysis of proteomics experiments. Current discovery-based mass spectrometry instrumentation in the facility is running at capacity causing long wait-times for service. Additionally, outdated instrumentation in the facility it being used for multiplexed proteomics and high-sensitivity experiments, but that instrumentation lacks the sensitivity and quality needed to properly support those experiments. In this application we are requesting the Orbitrap Eclipse w/FAIMS to replace a 9-year old Orbitrap Elite in order to achieve two goals: the first is to increase sample capacity/throughput of our facility to reduce wait-times and the second is to replace the outdated instrumentation to ensure discovery-based proteomics research is carried out on technically appropriate instrumentation. With TMT-based discovery experiments and analysis of major histocompatibility complex I (MHC-I) peptides being the most frequent requests for proteomics services, the Orbitrap Eclipse w/FAIMS is the most suitable instrument based on the instrument’s 1) scan speeds up to 40 Hz in the Orbitrap and 45 Hz in the ion trap for thorough sampling of complex peptide mixtures, 2) high ion transmission and ion mobility separations for high sensitivity, 3) real-time database searching for accurate multiplexed quantification, 4) new segmented quadrupole with hyperbolic rods for more accurate TMT quantification, and 5) novel active beam guide for enhanced sensitivity and robustness. This state-of-the art instrument would immediately support the research of 11 investigators funded by 14 NIH grants that include investigations identifying the proteins and protein modifications that regulate chromosome segregation, defining molecular pathways associated with energy balance, determining how mutations in RNA spliceosome proteins alter cellular phenotypes, understanding virulence factors associated with Group B streptococcus infection, identifying proteins that influence chimeric antigen receptor’s efficacy and side effects, and discovering protein biomarkers in ovarian cancer, breast cancer, and acute myeloid leukemia. Other projects aim to rapidly identify major MHC- I peptides to better understand immune system response, develop targeted therapies against myelodysplasia, leukemias, and other cancers driven by human papilloma virus infection, and better understand hematopoietic stem cell transplant outcomes in African American patients.