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.
Study ID | ST000909 |
Study Title | Metabolomics Linking Air Pollution, Obesity and Type 2 Diabetes |
Study Type | Untargeted high-resolution mass spectrometry profiling |
Study 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 | School of Medicine, Division of Pulmonary, Allergy, Critical Care Medicine |
Laboratory | Clincal Biomarkers Laboratory |
Last Name | Walker |
First Name | Douglas |
Address | 615 Michael St. Ste 225, Atlanta, GA, 30322, USA |
douglas.walker@emory.edu | |
Phone | (404) 727 5984 |
Submit Date | 2017-12-05 |
Total Subjects | 104 |
Study Comments | Both 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 Study | Yes |
Analysis Type Detail | LC-MS |
Release Date | 2020-09-12 |
Release Version | 1 |
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: | Mammals |
Factors:
Subject type: Plasma samples; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | HRM_Sample_Type |
---|---|---|
SA053064 | q3June2014_4b | Quality Control |
SA053065 | q3June2014_5a | Quality Control |
SA053066 | chearplasma_5a | Quality Control |
SA053067 | chearplasma_5b | Quality Control |
SA053068 | chearplasma_4f | Quality Control |
SA053069 | chearplasma_5c | Quality Control |
SA053070 | chearplasma_1d | Quality Control |
SA053071 | chearplasma_4b | Quality Control |
SA053072 | chearplasma_5d | Quality Control |
SA053073 | chearplasma_3b | Quality Control |
SA053074 | chearplasma_4e | Quality Control |
SA053075 | q3June2014_3a | Quality Control |
SA053076 | chearplasma_2a | Quality Control |
SA053077 | chearplasma_2b | Quality Control |
SA053078 | chearplasma_2f | Quality Control |
SA053079 | chearplasma_2e | Quality Control |
SA053080 | q3June2014_2a | Quality Control |
SA053081 | q3June2014_1b | Quality Control |
SA053082 | chearplasma_1c | Quality Control |
SA053083 | q3June2014_2b | Quality Control |
SA053084 | chearplasma_1e | Quality Control |
SA053085 | chearplasma_1f | Quality Control |
SA053086 | chearplasma_3a | Quality Control |
SA053087 | chearplasma_4a | Quality Control |
SA053088 | chearplasma_3c | Quality Control |
SA053089 | nist1 | Quality Control |
SA053090 | chearplasma_5e | Quality Control |
SA053091 | chearplasma_4d | Quality Control |
SA053092 | q3June2014_4a | Quality Control |
SA053093 | chearplasma_2d | Quality Control |
SA053094 | chearplasma_2c | Quality Control |
SA053095 | chearplasma_5f | Quality Control |
SA053096 | q3June2014_5b | Quality Control |
SA053097 | chearplasma_3f | Quality Control |
SA053098 | q3June2014_1a | Quality Control |
SA053099 | q3June2014_3b | Quality Control |
SA053100 | chearplasma_3e | Quality Control |
SA053101 | chearplasma_1a | Quality Control |
SA053102 | chearplasma_1b | Quality Control |
SA053103 | nist2 | Quality Control |
SA053104 | chearplasma_4c | Quality Control |
SA053105 | C-10TW8-S-00 | Study |
SA053106 | C-10XJ2-S-00 | Study |
SA053107 | C-10VE5-S-00 | Study |
SA053108 | C-10US5-S-00 | Study |
SA053109 | C-10WL9-S-00 | Study |
SA053110 | C-10UG2-S-00 | Study |
SA053111 | C-10TK4-S-00 | Study |
SA053112 | C-10WX2-S-00 | Study |
SA053113 | C-10W00-S-00 | Study |
SA053114 | C-10XH7-S-00 | Study |
SA053115 | C-10TA6-S-00 | Study |
SA053116 | C-10Z23-S-00 | Study |
SA053117 | C-10X82-S-00 | Study |
SA053118 | C-10SY4-S-00 | Study |
SA053119 | C-10TL2-S-00 | Study |
SA053120 | C-10TX5-S-00 | Study |
SA053121 | C-10T11-S-00 | Study |
SA053122 | C-10X09-S-00 | Study |
SA053123 | C-10YG8-S-00 | Study |
SA053124 | C-10U93-S-00 | Study |
SA053125 | C-10WY0-S-00 | Study |
SA053126 | C-10VR7-S-00 | Study |
SA053127 | C-10Y65-S-00 | Study |
SA053128 | C-10UU1-S-00 | Study |
SA053129 | C-10Z31-S-00 | Study |
SA053130 | C-10U69-S-00 | Study |
SA053131 | C-10V35-S-00 | Study |
SA053132 | C-10WW5-S-00 | Study |
SA053133 | C-10WB1-S-00 | Study |
SA053134 | C-10Z15-S-00 | Study |
SA053135 | C-10WM7-S-00 | Study |
SA053136 | C-10T03-S-00 | Study |
SA053137 | C-10YR4-S-00 | Study |
SA053138 | C-10T94-S-00 | Study |
SA053139 | C-10Y40-S-00 | Study |
SA053140 | C-10W18-S-00 | Study |
SA053141 | C-10YQ6-S-00 | Study |
SA053142 | C-10V43-S-00 | Study |
SA053143 | C-10VQ9-S-00 | Study |
SA053144 | C-10XR5-S-00 | Study |
SA053145 | C-10U51-S-00 | Study |
SA053146 | C-10YN2-S-00 | Study |
SA053147 | C-10YY8-S-00 | Study |
SA053148 | C-10VB2-S-00 | Study |
SA053149 | C-10WV7-S-00 | Study |
SA053150 | C-10TJ6-S-00 | Study |
SA053151 | C-10T78-S-00 | Study |
SA053152 | C-10XG9-S-00 | Study |
SA053153 | C-10YD4-S-00 | Study |
SA053154 | C-10VY1-S-00 | Study |
SA053155 | C-10V27-S-00 | Study |
SA053156 | C-10T86-S-00 | Study |
SA053157 | C-10VC0-S-00 | Study |
SA053158 | C-10W91-S-00 | Study |
SA053159 | C-10UR8-S-00 | Study |
SA053160 | C-10VM8-S-00 | Study |
SA053161 | C-10WK1-S-00 | Study |
SA053162 | C-10V19-S-00 | Study |
SA053163 | C-10U44-S-00 | Study |
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: | 100% water |
Solvent B: | 100% 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: | 100% water |
Solvent B: | 100% 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 |