Summary of Study ST000909

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 PR000630. The data can be accessed directly via it's Project DOI: 10.21228/M87H6H This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000909
Study TitleMetabolomics Linking Air Pollution, Obesity and Type 2 Diabetes
Study TypeUntargeted high-resolution mass spectrometry profiling
Study SummaryThe overall goal of this proposal is to use blood non-targeted high resolution metabolomics (HRM) to investigate the hypothesis that regional air pollution (NO2, PM2.5 and O3) and traffic-related air pollution exposures (traffic-related particulate matter components including EC2.5 and PM2.5 transition metals, and CALINE model-predicted NOx) alter key metabolic pathway(s) and that these alterations are associated with obesity and type 2 diabetes-related traits during the important developmental period of adolesence in the ongoing prospective Chidlren's Health study (CHS). Specific Aim 1 will examine the adverse impact of environmental chemicals in fasting blood samples measured by HRM on obesity (i.e., total body fat and body mass index (BMI)), metabolic dysfunction (e.g., fasting glucose and insulin concentrations and insulin resistance), and obesity-induced inflammation (i.e., leptin) among 104 Southern California adolescents enrolled in the CHS. Specific Aim 2 will examine associations of childhood exposures to PM2.5 and traffic-related air pollutants (i.e., CALINE model-predicted NOx) with biological metabolites identified in fasting blood samples using HRM among 104 adolescents in the CHS. Specific Aim 3 will investigate the metabolic pathways linking air pollution exposures and obesity and type 2 diabetes-related traits using pathway analysis under bayesian hierarchical model among 104 adolescents in the CHS.
Institute
Emory University
DepartmentSchool of Medicine, Division of Pulmonary, Allergy, Critical Care Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameWalker
First NameDouglas
Address615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Emaildouglas.walker@emory.edu
Phone(404) 727 5984
Submit Date2017-12-05
Total Subjects104
Study CommentsBoth CHEAR and Clinical Biomarker Laboratory pooled plasma samples were used for quality control. Study specific sample pools were not created
Raw Data File Type(s)mzXML
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2020-09-12
Release Version1
Douglas Walker Douglas Walker
https://dx.doi.org/10.21228/M87H6H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000630
Project DOI:doi: 10.21228/M87H6H
Project Title:Metabolomics Linking Air Pollution, Obesity and Type 2 Diabetes
Project Type:NIH/NIEHS P01-ES022845
Project Summary:The overall goal of this proposal is to use blood non-targeted high resolution metabolomics (HRM) to investigate the hypothesis that regional air pollution (NO2, PM2.5 and O3) and traffic-related air pollution exposures (traffic-related particulate matter components including EC2.5 and PM2.5 transition metals, and CALINE model-predicted NOx) alter key metabolic pathway(s) and that these alterations are associated with obesity and type 2 diabetes-related traits during the important developmental period of adolesence in the ongoing prospective Chidlren's Health study (CHS). Specific Aim 1 will examine the adverse impact of environmental chemicals in fasting blood samples measured by HRM on obesity (i.e., total body fat and body mass index (BMI)), metabolic dysfunction (e.g., fasting glucose and insulin concentrations and insulin resistance), and obesity-induced inflammation (i.e., leptin) among 104 Southern California adolescents enrolled in the CHS. Specific Aim 2 will examine associations of childhood exposures to PM2.5 and traffic-related air pollutants (i.e., CALINE model-predicted NOx) with biological metabolites identified in fasting blood samples using HRM among 104 adolescents in the CHS. Specific Aim 3 will investigate the metabolic pathways linking air pollution exposures and obesity and type 2 diabetes-related traits using pathway analysis under bayesian hierarchical model among 104 adolescents in the CHS.
Institute:Emory University
Department:Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Walker
First Name:Douglas
Address:615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Email:douglas.walker@emory.edu
Phone:(404) 727 5984
Funding Source:NIEHS ES026560
Contributors:Frank Gilliland University of Southern California Keck School of Medicine; Zhanghua Chen University of Southern California Keck School of Medicine; Dean P. Jones, Emory University School of Medicine

Subject:

Subject ID:SU000946
Subject Type:Plasma samples
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Pediatric samples
Human Trial Type:Observational
Species Group:Human

Factors:

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

mb_sample_id local_sample_id HRM_Sample_Type
SA053064q3June2014_4bQuality Control
SA053065q3June2014_5aQuality Control
SA053066chearplasma_5aQuality Control
SA053067chearplasma_5bQuality Control
SA053068chearplasma_4fQuality Control
SA053069chearplasma_5cQuality Control
SA053070chearplasma_1dQuality Control
SA053071chearplasma_4bQuality Control
SA053072chearplasma_5dQuality Control
SA053073chearplasma_3bQuality Control
SA053074chearplasma_4eQuality Control
SA053075q3June2014_3aQuality Control
SA053076chearplasma_2aQuality Control
SA053077chearplasma_2bQuality Control
SA053078chearplasma_2fQuality Control
SA053079chearplasma_2eQuality Control
SA053080q3June2014_2aQuality Control
SA053081q3June2014_1bQuality Control
SA053082chearplasma_1cQuality Control
SA053083q3June2014_2bQuality Control
SA053084chearplasma_1eQuality Control
SA053085chearplasma_1fQuality Control
SA053086chearplasma_3aQuality Control
SA053087chearplasma_4aQuality Control
SA053088chearplasma_3cQuality Control
SA053089nist1Quality Control
SA053090chearplasma_5eQuality Control
SA053091chearplasma_4dQuality Control
SA053092q3June2014_4aQuality Control
SA053093chearplasma_2dQuality Control
SA053094chearplasma_2cQuality Control
SA053095chearplasma_5fQuality Control
SA053096q3June2014_5bQuality Control
SA053097chearplasma_3fQuality Control
SA053098q3June2014_1aQuality Control
SA053099q3June2014_3bQuality Control
SA053100chearplasma_3eQuality Control
SA053101chearplasma_1aQuality Control
SA053102chearplasma_1bQuality Control
SA053103nist2Quality Control
SA053104chearplasma_4cQuality Control
SA053105C-10TW8-S-00Study
SA053106C-10XJ2-S-00Study
SA053107C-10VE5-S-00Study
SA053108C-10US5-S-00Study
SA053109C-10WL9-S-00Study
SA053110C-10UG2-S-00Study
SA053111C-10TK4-S-00Study
SA053112C-10WX2-S-00Study
SA053113C-10W00-S-00Study
SA053114C-10XH7-S-00Study
SA053115C-10TA6-S-00Study
SA053116C-10Z23-S-00Study
SA053117C-10X82-S-00Study
SA053118C-10SY4-S-00Study
SA053119C-10TL2-S-00Study
SA053120C-10TX5-S-00Study
SA053121C-10T11-S-00Study
SA053122C-10X09-S-00Study
SA053123C-10YG8-S-00Study
SA053124C-10U93-S-00Study
SA053125C-10WY0-S-00Study
SA053126C-10VR7-S-00Study
SA053127C-10Y65-S-00Study
SA053128C-10UU1-S-00Study
SA053129C-10Z31-S-00Study
SA053130C-10U69-S-00Study
SA053131C-10V35-S-00Study
SA053132C-10WW5-S-00Study
SA053133C-10WB1-S-00Study
SA053134C-10Z15-S-00Study
SA053135C-10WM7-S-00Study
SA053136C-10T03-S-00Study
SA053137C-10YR4-S-00Study
SA053138C-10T94-S-00Study
SA053139C-10Y40-S-00Study
SA053140C-10W18-S-00Study
SA053141C-10YQ6-S-00Study
SA053142C-10V43-S-00Study
SA053143C-10VQ9-S-00Study
SA053144C-10XR5-S-00Study
SA053145C-10U51-S-00Study
SA053146C-10YN2-S-00Study
SA053147C-10YY8-S-00Study
SA053148C-10VB2-S-00Study
SA053149C-10WV7-S-00Study
SA053150C-10TJ6-S-00Study
SA053151C-10T78-S-00Study
SA053152C-10XG9-S-00Study
SA053153C-10YD4-S-00Study
SA053154C-10VY1-S-00Study
SA053155C-10V27-S-00Study
SA053156C-10T86-S-00Study
SA053157C-10VC0-S-00Study
SA053158C-10W91-S-00Study
SA053159C-10UR8-S-00Study
SA053160C-10VM8-S-00Study
SA053161C-10WK1-S-00Study
SA053162C-10V19-S-00Study
SA053163C-10U44-S-00Study
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Collection:

Collection ID:CO000940
Collection Summary:Please contact project PI, Frank D. Gilliland (gillilan@usc.edu), for sample collection details.
Sample Type:Sodium Heparin Plasma
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000960
Treatment Summary:Samples were received frozen in aliquouts of <250uL. Freeze-thaw history for study samples prior to receipt by the Emory URR is provided in the Study Design section. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols described in the Sample Preparation section.

Sample Preparation:

Sampleprep ID:SP000953
Sampleprep Summary:Samples were prepared for metabolomics analysis using established methods (Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, urine aliquots were removed from storage at -80°C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 μL was transferred to a clean microfuge tube. Immediately after, the urine was treated with 100 μL of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 μL of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, urine was equilibrated for 30 min on ice, upon which precipitated proteins were removed by centrifuge (16.1 ×g at 4°C for 10 min). The resulting supernatant (100 μL) was removed, added to a low volume autosampler vial and maintained at 4°C until analysis (<22 h).
Sampleprep Protocol ID:HRM_SP_082016_01
Sampleprep Protocol Filename:EmoryUniversity_HRM_SP_082016_01.pdf
Sampleprep Protocol Comments:Date effective: 30 July 2016
Extraction Method:2:1 acetonitrile: sample followed by vortexing and centrifugation
Sample Spiking:2.5 uL [13C6]-D-glucose, [15N,13C5]-L-methionine, [13C5]-L-glutamic acid, [15N]-L-tyrosine, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine, [15N]-indole

Combined analysis:

Analysis ID AN001476 AN001477
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters XBridge Amide (50 x 2.1mm, 2.5um) Thermo Higgins C18 (50 x 2.1mm, 3um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH001035
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 μL of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Methods ID:2% formic acid in LC-MS grade water
Methods Filename:20160920_posHILIC120kres5min_ESI_c18negwash.meth
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge Amide (50 x 2.1mm, 2.5um)
Column Temperature:60C
Flow Gradient:A= water, B= acetontrile, C= 2% formic acid in water; 22.5% A, 75% B, 2.5% C hold for 1.5 min, linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min
Flow Rate:0.35 mL/min for 1.5 min; linear increase to 0.4 mL/min at 4 min, hold for 1 min
Sample Injection:10 uL
Solvent A:LC-MS grade water
Solvent B:LC-MS grade acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:HILIC
  
Chromatography ID:CH001036
Chromatography Summary:The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min.
Methods ID:10mM ammonium acetate in LC-MS grade water
Methods Filename:20160920_negC18120kres5min_ESI_HILICposwash.meth
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Thermo Higgins C18 (50 x 2.1mm, 3um)
Column Temperature:60C
Flow Gradient:A= water, B= acetontrile, C= 10mM ammonium acetate in water; 60% A, 35% B, 5% C hold for 0.5 min, linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3 min
Flow Rate:0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min
Sample Injection:10 uL
Solvent A:LC-MS grade water
Solvent B:LC-MS grade acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS001360
Analysis ID:AN001476
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:+3500
Activation Parameter:5e5
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Resolution Setting:120,000
Scanning Range:85-1275
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
  
MS ID:MS001361
Analysis ID:AN001477
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:-4000
Activation Parameter:5e5
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Resolution Setting:120,000
Scanning Range:85-1275
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
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