Quadrupole Time-of-Flight LC-MS

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Abstract This proposal is for the acquisition of a Bruker timsTOF Pro instrument to be placed in the Proteomics Shared laboratory Resource (SLR) at the Lerner Research Institute at the Cleveland Clinic. The Proteomics SLR is equipped with two LC-MS/MS systems including an eight year old ThermoScientific Orbitrap Elite and a three year old ThermoScientific Fusion Lumos system. The Proteomics SLR is currently running at capacity, with over 45% of the current experiments involving quantitative proteomic projects. The current workload of the Proteomics SLR has resulted in long wait times for proteomic experiments that involve the analysis of more than 20 samples. The large workload and subsequent wait times are exasperated by the low throughput workflow of the Elite and Lumos instruments, each instrument analyzing approximately 8 samples per day. The goal of this proposal is twofold and includes increasing the capacity of the Proteomics SLR and, more importantly, to expand the capabilities of the SLR to include high throughput proteomic experiments. The timsTOF Pro instrument is a fast scanning quadrupole time of flight instrument and was selected for this proposal based on data that indicates that this instrument can analyze between 40-100 samples per day without sacrificing proteome depth, sensitivity, accuracy and robustness. A comparison of a DIA based proteomic analysis of a tryptic digest generated from a cell lysate on the Lumos housed in the Proteomics SLR and the timsTOF Pro instrument showed that the timsTOF Pro quantified more proteins in a 30 minute gradient (over 4800) compared to a 90 minute gradient on the Lumos instrument (3000). This increased proteome depth is due to the higher scan rates, 100 Hz, of the timsTOF Pro, along with an additional dimension of separation (ion mobility), and the capability of this instrument to perform Parallel Accumulation Serial Fragmentation (PASEF) which allows synchronization of the quadrupole mass filter with the tims ion mobility cell. There are several studies that would benefit from access to the timsTOF Pro. These include studies of mouse models of alcohol-associated liver disease and non-alcoholic associated fatty liver disease (Nagy), the analysis of alterations to the sulhydrome that occur in ageing (Hine), a study of the signatures that are acutely altered by the gut microbe-derived metabolites TMA and TMAO (Brown), studies to better understand the mechanisms of glioblastoma (Lathia), identification of risk factors for major cardiovascular events (Hazen), identification of plasma biomarkers of severe asthma (Li), and the study of ECM remodeling that occurs in aortic aneurysms (AAA) and osteoarthritis (Apte).