PROJECT SUMMARY The long-term goal of this proposal is to advance the research of investigators at The Jackson Laboratory (JAX) and in the Maine research community by bringing a new Bruker timsTOF SCP mass spectrometer package for high-resolution, single-cell proteomic analysis to JAX’s Mass Spectrometry and Protein Chemistry Service (MSPC). JAX’s research mission focuses on discovering precise genomic solutions for disease to improve human health in the global community. As part of this mission, there has been an increasing emphasis on the analysis of single cells, as biomedical research has demonstrated that examination of biology at this level is essential for understanding the biological processes underlying development and disease. Accordingly, JAX has technologies for characterization and quantification of gene expression, chromatin accessibility, and individual cell-surface protein molecules present, all at the single-cell level. In addition, recently JAX investigators have had access to increasingly advanced capabilities in the MSPC in mass spectrometry-based proteomics and metabolomics for biological discoveries linking genomics with phenotype. However, despite our numerous mass spectrometry capabilities, there is currently no instrumentation here with the capability to perform unbiased, high-throughput label-free single-cell proteomics analysis. This gap limits our investigators’ ability to understand biology at the single-cell level, including new insights that would be gained by integrating single-cell proteome data with the array of other single-cell data generated here, and by addressing the issue of a generally weak transcriptome-proteome correlation in organisms. The Bruker timsTOF SCP mass spectrometer is the ideal system to address this gap. This instrument offers innovative technologies, including a dramatically improved ion-source concept, an enhanced trapped ion mobility, and mass analyzer that provide ultra-high sensitivity, enabling unbiased single-cell proteomics with high reproducibility. The timsTOF SCP can achieve coverage of about 1,500 proteins per cell, sufficiently identify post-translational modifications in a very small number of morphologically or functionally similar cells, and efficiently analyze low-abundant samples, such as the rare cell populations that many of our investigators study. The timsTOF SCP and its accessories, including the cellenONE for single-cell sorting and proteomic sample processing, will be transformative for research at JAX and other Maine research institutions. Various studies at JAX focused on rare immune-cell populations, stem-cell differentiation, sub-populations of cancer cells, the identification of new therapeutic targets for cancer, and characterizing mechanisms underlying cognitive aging will all benefit from this instrumentation. Progress in these research areas are particularly important given JAX’s broadening emphasis on translating our basic research discoveries into clinical advances that will directly benefit human health. In sum, the Bruker timsTOF SCP platform will substantially enhance JAX’s ability to fulfill its research mission and will also bring this potential to the greater Maine community.

PROJECT NARRATIVE Recent advances in biomedical research have demonstrated that analysis of single cells is essential for understanding the biological processes underlying development and disease. At The Jackson Laboratory (JAX), we have the capability to analyze diverse components in the pathways involved in protein production, including RNA and DNA molecules, and other molecules that modify levels of proteins generated from RNA or DNA, but currently we have no options for high-throughput identification of the “proteome,” i.e., the complete set of proteins, in a single cell. Access to the Bruker timsTOF SCP mass spectrometer and the accompanying cellenONE for sample processing requested in this application will provide investigators at both JAX and other Maine research institutions with access to a state-of-the-art single-cell proteomics system that will significantly advance research on a broad range of diseases.