Spatial proteomics of trace tissues isolated via LCM is limited by insufficient protein identification depth and coverage. We introduce a qMOFs-assisted protein preparation workflow into LCM-spatial proteomics, doubling the number of identified proteins (100 μm × 100 μm mouse myocardium) with high reproducibility. Building on this enhancement, we uncover cardiac aging-related cytoskeletal destabilization and mitochondrial dysregulation in perivascular myocardium, identifying Rack1 as a key node.