This article is available online at http://www.jlr.org be viewed relative to their location and intensity. As recently reviewed (9), MALDI-MSI of lipids has been quite successful, given that lipids are abundant in biological tissues. Additionally, with the exception of cardiolipins and gangliosides, lipids have molecular masses between 200 and 1,000 Da, an optimal operating mass range of MALDI-TOF instruments to achieve high mass resolving power and maintain accurate mass measurements.Niemann-Pick disease type C (NPC) is a fatal, neurodegenerative, lysosomal storage disorder caused by mutations of the encoding regions of genes either for the lysosomal transmembrane protein NPC1 or the cholesterol-binding glycoprotein NPC2 (10), two proteins that work in tandem to mobilize cholesterol through the late endosomal/lysosomal system (11)(12)(13)(14). As a result of the primary genetic defect, unesterified cholesterol and glycosphingolipids accumulate in late endosomes and lysosomes. Specifically, dysfunction of these proteins causes the inability to metabolize and traffic contents, and eventually cellular death. Cerebellar Purkinje neurons appear to be most susceptible though the cerebral cortex; thalamus and hippocampus also demonstrate neuronal loss (15)(16)(17)(18)(19). Systemic downstream effects include oxidative stress (20), defective calcium signaling (21), and neuroinflammation (22). The clinical phenotype of NPC is broad and includes vertical supranuclear gaze palsy, tremors, ataxia, and early dementia, and ultimately is fatal (23). While several studies have looked at transcript and protein-level alterations in NPC1 (22,(24)(25)(26)(27), less is known about alterations in the lipid landscape in the disease. Early work on lipid accumulation demonstrated that several tissues are affected (28-30). A targeted MS-based profiling study was reported in which different sphingolipids species were observed to be differential in the null NPC1 mouse model (31) as well as in the recently generated I1061T point mutant model (32).Abstract Mass spectrometry imaging (MSI) is a tool to rapidly map the spatial location of analytes without the need for tagging or a reporter system. Niemann-Pick disease type C1 (NPC1) is a neurodegenerative, lysosomal storage disorder characterized by accumulation of unesterified cholesterol and sphingolipids in the endo-lysosomal system. Here, we use MSI to visualize lipids including cholesterol in cerebellar brain tissue from the NPC1 symptomatic mouse model and unaffected controls. To complement the imaging studies, a data-processing pipeline was developed to generate consensus mass spectra, thereby using both technical and biological image replicates to assess differences. The consensus spectra are used to determine true differences in lipid relative abundance; lipid distributions can be determined in an unbiased fashion without prior knowledge of location. We show the cerebellar distribution of gangliosides GM1, GM2, and GM3, including variants of lipid chain length. We also performed MALDI-...