Metabolomic analysis data of MPP+-exposed SH-SY5Y cells using CE-TOFMS

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].


Specifications
Cellular and Molecular Neuroscience Specific subject area Metabolomic analysis Type of data Table  How data were acquired Capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) Data format Raw and analyzed data in the form of .xlsx file. Parameters for data collection Differentiated SH-SY5Y cells were treated with 0, 30 or 300 μM MPP + .
Samples were collected before treatment (0 hour) and after 24 h. Description of data collection Culture supernatants and methanol extracts from cells were ultrafiltered through 5 kDa cut-off membrane, and subjected to CE-TOFMS. Data source location Tokyo, Japan Data accessibility Culture supernatants: Supplementary

Value of the Data
• Both of extracellular and intracellular metabolic profiles provide an overview of the effect of MPP + exposure to differentiated SH-SY5Y cells, which is an established cellular model for Parkinson's disease (PD). • The data could be beneficial for researchers working on MPP + -exposed cellular PD models and MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine)-exposed animal PD models. • Metabolic changes elucidated using metabolomic analysis of a cellular PD model may provide our understanding about not only cellular and animal PD models, but also PD pathogenies. • Especially extracellular metabolic profiles may provide insight into seeking PD biomarker of body fluids like serum/plasma, cerebrospinal fluid or urine.

Data Description
MPTP is often used to produce animal models for Parkinson's disease (PD) because it produces selective loss of dopaminergic neurons in the substantia nigra and results in irreversible parkinsonism [2] . As a cellular model for PD, human neuroblastoma SH-SY5Y cells treated with MPP + , which is a toxic metabolite converted from MPTP, were widely used [3] . This article contains capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) metabolomic analysis data obtained from the culture supernatants and the cell lysate of MPP + -treated -SH-SY5Y cells [1] . The datasets containing compound name, database ID, m/z, migration time (MT) and relative peak area are provided in Supplementary Table 1A (culture supernatant) and 2A (cell lysate). The relative quantification data of main metabolites are also provided in Supplementary Table 1B (culture supernatant) and 2B (cell lysate). Sigma) was added for 24 h. Samples of culture supernatant and cell lysate were collected before treatment (0 h) and after 24 h, and then subjected to metabolite extraction (each n = 3, except n = 6 for 0 h-culture supernatant).

Metabolite extraction and metabolomic analysis
The supernatants of culture media were collected and an internal standard (Human Metabolome Technologies (HMT; Yamagata, Japan) was added to them. To remove macromocleules, ultrafiltration was employed using 5 kDa cut-off membrane (UltrafreeMC-PLHCC, HMT) at 9100 × g for 1 h at 4 °C. The filtrate was then provided for metabolomic analysis.
After removing culture supernatant, the cells grown in 90 mm dishes were washed with 10 mL of 5% mannitol solution. Second wash was employed with 2 mL of 5% mannitol solution.
The metabolites were extracted with 800 μL of methanol (LC-MS grade) and then 550 μL of water containing internal standard (HMT) was added. 10 0 0 μL of the mixtures were collected and centrifuged at 2300 × g for 5 min at 4 °C. Next, 700 μL of the supernatants were subjected to ultrafiltration to remove macromolecules. The ultrafiltration was employed using 5 kDa cutoff membrane (UltrafreeMC-PLHCC, HMT) at 9100 × g for 2 h at 4 °C. The filtrate was then dried and reconstituted in 25 μL Milli-Q water prior to metabolomic analysis.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.