In summary, by the MS-based differential quantitative proteomics, we revealed that the dysfunction of Npc1 is not only associated with a reduced expression of various myelin structural and indispensable proteins (Bcas1, Enpp6, Mbp, and Ugt8) but also the proteins (Cers2, Ugt8, and Gltp) related to sphingolipid metabolism in NPC mice. The gene discussed is ENPP6; the disease is nasopharyngeal carcinoma.