Mass spectrometry-based lipid analysis in NPC1 disease: Methods for phosphoinositide quantification, lipid imaging, and myelin lipid profiling.

Loss of NPC cholesterol transporter 1 protein function results in severe lipid dysregulation in multiple vital organs, including the brain, in Niemann-Pick Type C1 (NPC1) disease. Investigation of lipid changes and lipid metabolism disruptions in NPC1 is critical to elucidating the disease mechanisms driving the pathophysiology, identifying potential biomarkers, and guiding therapeutic strategies. One such example is phosphoinositides, which are key lipids involved in multiple signaling pathways relevant to NPC1 that are challenging to study due to their low abundance and detection difficulty. In this chapter, we present a detailed phosphoinositide analysis protocol using mass spectrometry. When studying lipids, spatial information is also important because it reveals distribution within the tissue, which can provide insights into functional roles and disease-related alterations. MALDI-MS lipid imaging is a powerful tool for investigating the spatial distribution of lipids. Herein, we also discuss a protocol for lipid imaging using MALDI-MSI, along with key precautions and troubleshooting tips. Finally, we present a myelin isolation protocol integrated with LC-MS lipidomics to investigate the myelin lipidome in tissues such as the brain, as myelin lipid composition is crucial for maintaining neuronal function and is often disrupted in neurodegenerative diseases like NPC1, including the investigation of phosphoinositides.