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/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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Project:

Project ID:PR000416
Project DOI:doi: 10.21228/M88S3F
Project Title:Metabolomic study on a schizophrenia and type 2 diabetes susceptibility gene Nos1AP-rs12742393
Project Summary: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 Name:Zhang
First Name:Yinan
Address:600 Yishan Road
Email:zhyn@sjtu.edu.cn
Phone:18616691438

Subject:

Subject ID:SU000590
Subject Type:serum
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Subject type: serum; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA029754X264_1AA
SA029755X263_1AA
SA029756X265_1AA
SA029757X266_1AA
SA029758X268_1AA
SA029759X262_1AA
SA029760X261_1AA
SA029761X257_1AA
SA029762X258_1AA
SA029763X259_1AA
SA029764X260_1AA
SA029765X269_1AA
SA029766X270_1AA
SA029767X277_1AA
SA029768X278_1AA
SA029769X279_1AA
SA029770X231_1AA
SA029771X276_1AA
SA029772X275_1AA
SA029773X271_1AA
SA029774X272_1AA
SA029775X273_1AA
SA029776X274_1AA
SA029777X256_1AA
SA029778X267_1AA
SA029779X239_1AA
SA029780X238_1AA
SA029781X240_1AA
SA029782X241_1AA
SA029783X242_1AA
SA029784X237_1AA
SA029785X236_1AA
SA029786X232_1AA
SA029787X255_1AA
SA029788X234_1AA
SA029789X235_1AA
SA029790X243_1AA
SA029791X233_1AA
SA029792X250_1AA
SA029793X251_1AA
SA029794X252_1AA
SA029795X244_1AA
SA029796X249_1AA
SA029797X253_1AA
SA029798X245_1AA
SA029799X254_1AA
SA029800X246_1AA
SA029801X248_1AA
SA029802X247_1AA
SA029803X312_1AC
SA029804X315_1AC
SA029805X311_1AC
SA029806X314_1AC
SA029807X313_1AC
SA029808X308_1AC
SA029809X316_1AC
SA029810X306_1AC
SA029811X307_1AC
SA029812X309_1AC
SA029813X310_1AC
SA029814X322_1AC
SA029815X326_1AC
SA029816X325_1AC
SA029817X327_1AC
SA029818X328_1AC
SA029819X305_1AC
SA029820X324_1AC
SA029821X323_1AC
SA029822X318_1AC
SA029823X319_1AC
SA029824X320_1AC
SA029825X321_1AC
SA029826X317_1AC
SA029827X304_1AC
SA029828X287_1AC
SA029829X286_1AC
SA029830X288_1AC
SA029831X289_1AC
SA029832X290_1AC
SA029833X285_1AC
SA029834X284_1AC
SA029835X303_1AC
SA029836X281_1AC
SA029837X282_1AC
SA029838X283_1AC
SA029839X291_1AC
SA029840X280_1AC
SA029841X300_1AC
SA029842X301_1AC
SA029843X302_1AC
SA029844X292_1AC
SA029845X298_1AC
SA029846X299_1AC
SA029847X297_1AC
SA029848X293_1AC
SA029849X295_1AC
SA029850X294_1AC
SA029851X296_1AC
SA029852X214_1CC
SA029853X215_1CC
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Collection:

Collection ID:CO000584
Collection Summary:A total of 147 healthy subjects with normal glucose tolerance were included in this study, including 49 subjects of CC homozygotes, 49 subjects of AC heterozygotes, and 49 subjects of AA homozygotes. All subjects included in this study for the metabolomic analysis were matched for age, sex, body mass index (BMI). Serum samples were collected after 8h fasting and stored at −80 °C until analysis. Pooled quality control (QC) samples were prepared by mixing all serum samples from every participant (20 μL each) and then analyzed.
Sample Type:Blood

Treatment:

Treatment ID:TR000604
Treatment Summary:Serum samples were collected after 8h fasting and stored at −80 °C until analysis. Pooled quality control (QC) samples were prepared by mixing all serum samples from every participant (20 μL each) and then analyzed.

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.

Combined analysis:

Analysis ID AN000873 AN000874 AN000875
Analysis type MS MS MS
Chromatography type GC Reversed phase Reversed phase
Chromatography system Agilent 6890N Waters Waters
Column DB-5MS capillary column Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um)
MS Type EI ESI ESI
MS instrument type GC x GC-TOF QTOF QTOF
MS instrument name Agilent Waters Waters
Ion Mode POSITIVE POSITIVE NEGATIVE
Units peak area peak height peak height

Chromatography:

Chromatography ID:CH000620
Instrument Name:Agilent 6890N
Column Name:DB-5MS capillary column
Chromatography Type:GC
  
Chromatography ID:CH000621
Instrument Name:Waters
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS000774
Analysis ID:AN000873
Instrument Name:Agilent
Instrument Type:GC x GC-TOF
MS Type:EI
Ion Mode:POSITIVE
  
MS ID:MS000775
Analysis ID:AN000874
Instrument Name:Waters
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000776
Analysis ID:AN000875
Instrument Name:Waters
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
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