1-Methyl-4-phenylpyridinium (MPP+)-treated human neuroblastoma SH-SY5Y cells have been generally accepted as a cellular model for Parkinson's disease. This article contains metabolic analysis data of not only cell lysate but also culture supernatants to understand comprehensive metabolic disturbances in this model. Metabolic analysis employed by capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). Data obtained by CE-TOFMS were processed to extract peak information including m/z, peak area, and migration time. The data provided in this manuscript have been analyzed and discussed in the research article entitled "Metabolomic analysis revealed mitochondrial dysfunction and aberrant choline metabolism in MPP+-exposed SH-SY5Y cells" [1].