DISCO-MS: Proteomics of spatially identified tissues in whole organs

Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. Liquid chromatography coupled to mass spectrometry (LC-MS) is emerging as a key technology for the unbiased characterization of proteins, the drivers of cellular function. Furthermore, recent advances in imaging, transcriptomics and proteomics allowed the analysis of spatially resolved RNA- and protein-profiles from thin tissue sections. However, so far, no method has allowed the unbiased mass spectrometry (MS)-based proteomics analysis of target tissues identified by unbiased imaging of whole organs in 3D. Here, we present DISCO-MS, a technology combining solvent-based tissue clearing, whole-organ imaging by light-sheet microscopy, automated image analysis powered by deep learning, and ultra-high sensitivity mass spectrometry. DISCO-MS yields qualitative and quantitative proteomics data indistinguishable from uncleared samples in both rodent and human tissue. DISCO-MS of the proteomes of axonal tracts with activated microglia after brain injury revealed known and novel biomarkers. We characterized individual initial amyloid beta plaques in the brains of a young familial Alzheimer's disease mouse model, determined the core proteome of these aggregates and highlighted compositional heterogeneity. DISCO-MS enables the image-guided identification of rare target tissues in intact biological systems followed by MS-based proteome analysis, providing new diagnostic and therapeutic opportunities for complex diseases including neurodegeneration.