Integrated laser ablation and droplet collection system for efficient single cell isolation v1

State-of-the-art omics and imaging technologies for transcriptome, epigenome, and proteome measurements at the single-cell level have been successfully demonstrated and integrated into large tissue mapping consortia (e.g., HuBMAP, SenNet). However, current approaches for probing spatial distribution of the proteome typically rely on the use of antibodies, which limits multiplexing and requires a priori knowledge of protein targets. In this protocol, we describe a novel MS based spatial proteomic approach and deploy it for unbiased and deep mapping of proteins in tissues and specifically within senescent cells and their surrounding tissue microenvironment. The spatial single-cell proteomics (SSCP) technology enables efficient sample collection at high spatial resolution (5-10 μm) and opens the door to global cellular, subcellular and organelle proteomics. This approach is demonstrated here applied to a mouse tissue sample.