Metal-Organic Framework Assisted Sample Preparation Enables High-Depth Proteomics of Laser-Captured Trace Kidney...

Region-resolved proteomics based on laser capture microdissection (LCM) enables molecular characterization of solid organ heterogeneity but is limited by severe protein loss and shallow coverage in trace tissue samples. Here, we adapted and optimized a quadruple boronic acid-rich lanthanide metal-organic framework (qMOFs)-aided sample preparation workflow (MASP) for LCM-derived trace kidney tissues and benchmarked its performance against conventional filter-aided sample preparation (FASP) across tissue inputs of 0.25-1.5 mm². Notably, MASP identified at least 6248 protein groups from 0.25 mm² of tissue, approximately three times the maximum number of 2042 protein groups identified by FASP from 1.5 mm² of tissue. We further applied this workflow to region-resolved proteomic profiling of renal cortex and medulla in a cecal ligation and puncture (CLP)-induced sepsis-associated acute kidney injury (SA-AKI) mouse model, identifying regional proteomic differences between cortical and medullary microregions and changes in mitochondrial protein abundance in cortical samples from Sham and CLP mice. This work extends MASP to microdissected solid tissues and provides a robust platform for high-depth region-resolved proteomics of heterogeneous organs, enabling systematic investigation of region-specific molecular alterations in disease.