We used a novel MALDI MSI setup with trapped ion mobility separation (TIMS) to further resolve plaque associated lipid species. The MSI experiments were interfaced with fluorescent amyloid staining on the same section using electrooptic amyloid probes, luminescent conjugated oligothiophenes (LCOs) ) that allow to delineate structurally different amyloid aggregates . This hyperspectral imaging approach identified distinct lipid localization patterns specific to polymorphic amyloid structures including mass overlapping compounds, which could be further resolved by ion mobility separation.