Hybrid ESI/MALDI mass spectrometer with trapped ion mobility spectrometry

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The application aims to provide adequate instrumentation for the applicants’ research program in translational/clinical proteomics and in mass spectrometry imaging. The translational/clinical proteomics arm employs liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) while the mass spectrometry imaging arm employs matrix assisted laser desorption/ionization (MALDI). In order to foster synergies of the two approaches as well as for efficient instrument usage and to optimize spatial footprint and cost effectiveness, a hybrid ESI/MALDI system is proposed. The applicants include an established and a junior research group as well as a proteomic core facility. As Heisenberg Professor for Translational Proteomics at the Institute of Surgical Pathology, the lead applicant is ideally positioned to foster high-throughput clinical proteomics. Selected research projects aim to characterize the proteome biology of solid tumors for risk stratification and pathomechanistic understanding. Research projects also include serum proteome profiling. Proof-of-concept data is provided. The scarcity of clinical specimens and the need to study large patient cohorts necessitate sensitive proteomics and fast throughput. MALDI imaging serves to better understand tissue heterogeneity in tumor pathobiology at close to single-cell resolution. MALDI imaging seamlessly integrates into clinical proteomics studies by providing insights into spatial proteome biology directly from patient tissues. The junior research group ‘MALDI Imaging’ will investigate spatially resolved molecular processes in highly aggressive solid tumors. This includes characterization of intra-tumor heterogeneity, unraveling pathobiological processes inside the tumor and tumor microenvironment as well as the identification of spatio-molecular markers for diagnostic and prognostic patient stratification. Spatial omics analyses will include imaging of small molecules such as metabolites, lipids, drugs, and drug metabolites. For these small molecules, MALDI imaging allows label-free, multiplexed spatially resolved measurements. The Core Facility makes proteomics accessible to the wider scientific community with a focus on clinical scientists. To successfully accomplish the research programme in translational/clinical proteomics, including spatial multi-omics, state-of-the-art mass spectrometry is required with the following key features: • Hybrid system to cover LC-ESI-MS/MS and MALDI-MS • Trapped Ion Mobility Spectrometry (TIMS) for improved in situ MALDI imaging • Parallel Accumulation Serial Fragmentation (PASEF) for efficient ion usage from scarce clinical samples •Fast acquisition speed for improved throughput of large clinical sample cohorts, achieved by running shorter gradients while maintaining high proteome coverage • Fast laser frequency and high spatial resolution for MALDI imaging • Vacuum MALDI in order to build on the established research program.