Summary of Study ST000568

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000416. The data can be accessed directly via it's Project DOI: 10.21228/M88S3F This work is supported by NIH grant, U2C- DK119886.

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Study IDST000568
Study TitleMetabolomic study on a schizophrenia and type 2 diabetes susceptibility gene
Study Summarya comprehensive serum metabolomic analysis in healthy subjects with different genotypes of rs12742393 (n=49 for AA, AC, and CC, respectively) using gas chromatography–time-of-flight mass spectrometry and ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry.
Institute
Shanghai Jiao Tong University Affiliated Sixth People’s Hospital
Last NameZhang
First NameYinan
Address600 Yishan Road
Emailzhyn@sjtu.edu.cn
Phone86-21-24056374
Submit Date2017-01-15
Study CommentsNOS1AP variant rs12742394
Analysis Type DetailGC-MS/LC-MS
Release Date2017-07-10
Release Version1
Yinan Zhang Yinan Zhang
https://dx.doi.org/10.21228/M88S3F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP000597
Sampleprep Summary:Sample preparation and analysis by GC-TOFMS: Samples were derivatized and subsequently analyzed by GC-TOFMS following our previously published protocols with minor modifications (Qiu, Cai, Su, Chen, Zheng, Xu, Ni et al. 2009). Briefly, a 100 μL aliquot of serum sample was extracted with 300 μL of methanol: chloroform (3:1) and vortexed for 30 s. After keeping the extract for 10 min at -20 °C, the samples were centrifuged at 12,000 rpm for 10 min. An aliquot of the 300 μL supernatant was transferred to a glass sampling vial, and was spiked with one internal standards (10 μL L-4-chlorophenylalanine in water, 0.3 mg/mL) to vacuum dry at room temperature. The residue was derivatized using a two-step procedure. First, 80 μL methoxyamine (15 mg/mL in pyridine,) was added to the vial and kept at 30 °C for 90 min, second, 80 μL BSTFA (1%TMCS) was added and kept at 70°C for 60 min. Each 1 μL aliquot of the derivatized solution was injected in spitless mode into an Agilent 6890N GC coupled with a Pegasus HT TOFMS (Leco Corp., St. Joseph, MI, USA). The samples were run in the order of AA-AC-CC, alternately, to minimize systematic analytical deviations. One QC sample and one blank vial were run after each 10 test serum samples. Separation was achieved on a DB-5MS capillary column (30 m × 250 µm I.D., 0.25-µm film thickness; (5%-phenyl)-methylpolysiloxane bonded and cross linked; Agilent J&W Scientific, Folsom, CA, USA) with helium as the carrier gas at a constant flow rate of 1.0 mL/min. The temperature of injection, transfer interface, and ion source was set to 270 °C, 270 °C, and 220 °C, respectively. The GC temperature programming was set to 2 min isothermal heating at 80 °C, followed by 10 °C/min oven temperature ramps to 180 °C, 6 °C/min to 230 °C, and 40 °C/min to 295 °C, and a final 8 min maintenance at 295 °C. Electron impact ionization (70 eV) at full scan mode (m/z 30-600) was used, with an acquisition rate of 20 spectra/sec in the TOFMS setting. Sample preparation and analysis by UPLC-QTOFMS: Sample preparation and analysis with UPLC-QTOF-MS was performed according to our published report with minor modifications (Qiu, Cai, Su, Chen, Zheng, Xu, Ni et al. 2009). An aliquot of 40 μL serum was spiked with 20 μL of internal standard (L-4-chlorophenylalanine in water, 30 μg/mL), and extracted with 500 μL of acetonitrile and methanol (9:1) respectively. After vortexing for 2 min, the mixture was kept at -20°C for 10 min, and then centrifuged at 12,000 rpm for 20 min. The supernatant was transferred into the sampling vial pending UPLC-QTOFMS (Waters Corp., Milford, MA, USA) analysis. All the samples were kept at 4°C before injection. An aliquot of 5 µL filtrate was injected at an order of AA-AC-CC, alternately, into a 100 mm×2.1mm, 1.7μm BEH C18 column (Waters Corp., Milford, MA, USA) held at 40°C using an UPLC system (Waters Corp., Milford, MA, USA). One QC sample and one blank vial were run after each 10 serum samples. The column was eluted with a linear gradient of 1-20% B over 0-1 min, 20-70% B over 1-3 min, 70-85% B over 3-8 min, 85-100% B over 8-9 min, the fluent was held at 100% B for 1 min. For electrospray positive ion mode (ES+) analysis, mobile phase was water with 0.1% formic acid, B was acetonitrile with 0.1% formic acid, while A with water and B with acetonitrile for negative ion mode (ES-) analysis. The flow rate was 0.4 mL/min. All the samples were kept at 4 °C during the analysis. The mass spectrometric data were collected using a Waters Q-TOF Premier (Waters Corp., Milford, MA, USA) equipped with an electrospray source operating in either ES+ or ES-. The source temperature was set at 120°C with a cone gas flow of 50 L/h, a desolvation gas temperature of 350°C with a desolvation gas flow of 650 L/h. In the case of positive and negative ion mode, the capillary voltage was set to 3.2 kV and 3 kV, and the cone voltage of 35 V and 50 V, respectively. Centroid data were collected from 50 to 1000 m/z with a scan time of 0.3 s and interscan delay of 0.02 s over a 9.5 min analysis time. MassLynx software (Waters Corp., Milford, MA, USA) was used for system controlling and data acquisition. Leucine enkephalin was used as the lock mass (m/z 556.2771 in ES+ and 554.2615 in ES-) at a concentration of 100 ng/mL and a flow rate of 0.02 mL/min for all analyses. The samples were run in the order of AA-AC-CC, alternately, to minimize systematic analytical deviations. One QC sample and one blank vial were run after each ten serum test samples.
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