Summary of Study ST001004

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 PR000679. The data can be accessed directly via it's Project DOI: 10.21228/M8X10M 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 IDST001004
Study TitleDenver Asthma Panel Study-CHEAR Ancillary Study
Study TypeUntargeted high-resolution mass spectrometry profiling
Study SummaryUrban environments remain a poorly understood toxic environment for children with asthma, where improved exposure characterization and estimation of exposurehealth outcome relationships are clearly needed. The goal of this project is to investigate the interactions between relevant environmental exposures and asthma severity in a year-long longitudinal study of urban children with asthma. Environmental and clinical samples are being collected at 3 seasonal visits. Using these samples, we will measure the effects of multiple relevant exposures (environmental tobacco smoke (ETS), polycyclic aromatic hydrocarbons (PAHs), phthalates, and volatile organic compounds (VOCs)) on biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids) and asthma outcomes. Our overall hypothesis is that relevant environmental exposures and their interactions drive disease severity in urban children with asthma. We will test this hypothesis by investigating the following aims: Aim 1: To investigate how environmental exposures (ETS, PAHs, phthalates, and VOCs) and their interactions contribute to asthma severity in urban children. Aim 2: To determine if environmental exposures in children with asthma are associated with changes in in biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids). Aim 3: To determine which biological responses mediate the relationships between environmental exposures and asthma severity. Aim 4: To compare environmental exposures and biological responses in asthmatic and non-asthmatic children
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameUppal
First NameKaran
Address615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Emailkuppal2@emory.edu
Phone(404) 727 5027
Submit Date2018-06-21
Total Subjects66
Study CommentsBoth CHEAR and Clinical Biomarker Laboratory pooled plasma samples were used for quality control. Study specific sample pools were not created
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2021-08-31
Release Version1
Karan Uppal Karan Uppal
https://dx.doi.org/10.21228/M8X10M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000679
Project DOI:doi: 10.21228/M8X10M
Project Title:Denver Asthma Panel Study-CHEAR Ancillary Study
Project Type:NIH/NIEHS 1U2CES026560-01
Project Summary:Urban environments remain a poorly understood toxic environment for children with asthma, where improved exposure characterization and estimation of exposurehealth outcome relationships are clearly needed. The goal of this project is to investigate the interactions between relevant environmental exposures and asthma severity in a year-long longitudinal study of urban children with asthma. Environmental and clinical samples are being collected at 3 seasonal visits. Using these samples, we will measure the effects of multiple relevant exposures (environmental tobacco smoke (ETS), polycyclic aromatic hydrocarbons (PAHs), phthalates, and volatile organic compounds (VOCs)) on biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids) and asthma outcomes. Our overall hypothesis is that relevant environmental exposures and their interactions drive disease severity in urban children with asthma. We will test this hypothesis by investigating the following aims: Aim 1: To investigate how environmental exposures (ETS, PAHs, phthalates, and VOCs) and their interactions contribute to asthma severity in urban children. Aim 2: To determine if environmental exposures in children with asthma are associated with changes in in biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids). Aim 3: To determine which biological responses mediate the relationships between environmental exposures and asthma severity. Aim 4: To compare environmental exposures and biological responses in asthmatic and non-asthmatic children
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Uppal
First Name:Karan
Address:615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Email:kuppal2@emory.edu
Phone:(404) 727 5027
Funding Source:NIEHS ES026560
Contributors:Andrew Lui (University of Colorado Denver), Tasha Fingerlin ( University of Colorado Denver), Jonathon Thornburg (University of Colorado Denver), and Dean P. Jones (Emory University)

Subject:

Subject ID:SU001089
Subject Type:Plasma samples
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Teens (12 – 17 yr)

Factors:

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

mb_sample_id local_sample_id HRM_Sample_Type
SA070977q3June2014_2b_1Quality Control
SA070978chearplasma_2f_1Quality Control
SA070979nist2_1Quality Control
SA070980q3June2014_1a_2Quality Control
SA070981chearplasma_1a_2Quality Control
SA070982chearplasma_2e_1Quality Control
SA070983nist1_1Quality Control
SA070984chearplasma_2c_1Quality Control
SA070985q3June2014_1b_1Quality Control
SA070986chearplasma_1f_1Quality Control
SA070987q3June2014_2a_1Quality Control
SA070988chearplasma_2a_1Quality Control
SA070989chearplasma_1b_2Quality Control
SA070990chearplasma_2b_1Quality Control
SA070991chearplasma_2d_1Quality Control
SA070992chearplasma_1c_2Quality Control
SA070993chearplasma_2d_2Quality Control
SA070994chearplasma_2c_2Quality Control
SA070995chearplasma_2e_2Quality Control
SA070996chearplasma_2f_2Quality Control
SA070997nist2_2Quality Control
SA070998q3June2014_2b_2Quality Control
SA070999chearplasma_2b_2Quality Control
SA071000chearplasma_2a_2Quality Control
SA071001chearplasma_1e_2Quality Control
SA071002chearplasma_1d_2Quality Control
SA071003chearplasma_1f_2Quality Control
SA071004q3June2014_1b_2Quality Control
SA071005q3June2014_2a_2Quality Control
SA071006chearplasma_1e_1Quality Control
SA071007nist1_2Quality Control
SA071008chearplasma_1c_1Quality Control
SA071009chearplasma_1b_1Quality Control
SA071010chearplasma_1d_1Quality Control
SA071011chearplasma_1a_1Quality Control
SA071012q3June2014_1a_1Quality Control
SA071013C-1G900-P-00_1Study
SA071014C-1G9J3-P-00_1Study
SA071015C-1FXR7-P-00_2Study
SA071016C-1G1R4-P-00_2Study
SA071017C-1G306-P-00_1Study
SA071018C-1G6T4-P-00_2Study
SA071019C-1G8A4-P-00_1Study
SA071020C-1G8P1-P-00_2Study
SA071021C-1G9E4-P-00_2Study
SA071022C-1G199-P-00_2Study
SA071023C-1G397-P-00_2Study
SA071024C-1G1P8-P-00_2Study
SA071025C-1G850-P-00_1Study
SA071026C-1G108-P-00_1Study
SA071027C-1G470-P-00_2Study
SA071028C-1G5P4-P-00_2Study
SA071029C-1FXC0-P-00_2Study
SA071030C-1G6A6-P-00_2Study
SA071031C-1FZY9-P-00_2Study
SA071032C-1G6J6-P-00_1Study
SA071033C-1G0G9-P-00_2Study
SA071034C-1FYH8-P-00_1Study
SA071035C-1G7U1-P-00_2Study
SA071036C-1G033-P-00_2Study
SA071037C-1FY00-P-00_2Study
SA071038C-1FX76-P-00_2Study
SA071039C-1G579-P-00_2Study
SA071040C-1G0N3-P-00_2Study
SA071041C-1G3C5-P-00_2Study
SA071042C-1GB35-P-00_2Study
SA071043C-1G8Q9-P-00_2Study
SA071044C-1G6M0-P-00_2Study
SA071045C-1G041-P-00_2Study
SA071046C-1G4E9-P-00_2Study
SA071047C-1G7H0-P-00_2Study
SA071048C-1G330-P-00_2Study
SA071049C-1FZL8-P-00_2Study
SA071050C-1G678-P-00_2Study
SA071051C-1G9L9-P-00_2Study
SA071052C-1G8X3-P-00_2Study
SA071053C-1FXX3-P-00_2Study
SA071054C-1FYU9-P-00_1Study
SA071055C-1G4M2-P-00_1Study
SA071056C-1FXD7-P-00_2Study
SA071057C-1G876-P-00_2Study
SA071058C-1G5S7-P-00_2Study
SA071059C-1G6V0-P-00_2Study
SA071060C-1G405-P-00_2Study
SA071061C-1GB19-P-00_2Study
SA071062C-1GAV9-P-00_2Study
SA071063C-1G4F7-P-00_2Study
SA071064C-1G363-P-00_2Study
SA071065C-1G124-P-00_2Study
SA071066C-1G181-P-00_2Study
SA071067C-1G2W2-P-00_2Study
SA071068C-1G6L2-P-00_2Study
SA071069C-1FYC9-P-00_2Study
SA071070C-1FYY0-P-00_2Study
SA071071C-1G785-P-00_2Study
SA071072C-1G9V7-P-00_1Study
SA071073C-1G1G8-P-00_1Study
SA071074C-1G3D2-P-00_2Study
SA071075C-1G1N2-P-00_2Study
SA071076C-1FYK1-P-00_2Study
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Collection:

Collection ID:CO001083
Collection Summary:Blood plasma samples were collected from nonfasting participants in the Denver Asthma Panel Study at enrollment (baseline). Blood samples were collected in tubes containing EDTA and after centrifugation aliquots of plasma were transferred to 1.8 ml freezer tubes and stored in a -70 degrees C freezer.
Sample Type:Plasma - EDTA
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001103
Treatment Summary:Samples were received frozen in aliquouts of <250uL. 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:SP001096
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, plasma aliquots were removed from storage at -80 degrees C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 microliters was transferred to a clean microfuge tube. Immediately after, the plasma was treated with 100 microliters of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 microliters 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 (14,000 rpm at 4 degrees C for 10 min). The resulting supernatant (100 microliters) was removed, added to a low volume autosampler vial and maintained at 4 degrees 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

Combined analysis:

Analysis ID AN001714 AN001715
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters XBridge BEH Amide XP HILIC (50 x 2.1mm,2.5um) with Thermo Accucore HILIC guard Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
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 Area Peak Area

Chromatography:

Chromatography ID:CH001210
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 microliters 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 BEH Amide XP HILIC (50 x 2.1mm,2.5um) with Thermo Accucore HILIC guard
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:CH001211
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:Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
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:MS001586
Analysis ID:AN001714
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:5.00E+05
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:MS001587
Analysis ID:AN001715
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:5.00E+05
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:MS001669
Analysis ID:AN001714
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:5.00E+05
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:MS001670
Analysis ID:AN001715
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:5.00E+05
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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