Summary of study ST001079

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 PR000722. The data can be accessed directly via it's Project DOI: 10.21228/M8BT3D 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 IDST001079
Study TitleEnvironmental exposures and inflammation in young children with cystic fibrosis
Study TypeUntargeted high-resolution mass spectrometry profiling
Study SummarySecondhand smoke exposure (SHSe) is a common environmental factor known to increase asthma severity and respiratory infections in children, as well disrupt metabolic signals and host immune responses in patients with cystic fibrosis (CF). This study defines biomarkers and metabolic profiles of SHSe (includes ENDS exposure) in the young CF population and determines how SHSe impacts regulation of infection, inflammation, and respiratory health.
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameMa
First NameChunyu
Address615 Michael St. Ste 225, Atlanta, GA, 30322, USA
Emailchunyu.ma@emory.edu
Phone(404) 727 5091
Submit Date2018-10-10
Total Subjects92
Study CommentsBoth CHEAR and Clinical Biomarkers Laboratory pooled plasma samples were used for quality control. Study specific sample pools were not created
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2019-10-11
Release Version1
Chunyu Ma Chunyu Ma
https://dx.doi.org/10.21228/M8BT3D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000722
Project DOI:doi: 10.21228/M8BT3D
Project Title:Environmental exposures and inflammation in young children with cystic fibrosis
Project Type:NIH/NIEHS 1U2CES026560-01
Project Summary:Secondhand smoke exposure (SHSe) is a common environmental factor known to increase asthma severity and respiratory infections in children, as well disrupt metabolic signals and host immune responses in patients with cystic fibrosis (CF). This study defines biomarkers and metabolic profiles of SHSe (includes ENDS exposure) in the young CF population and determines how SHSe impacts regulation of infection, inflammation, and respiratory health.
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Ma
First Name:Chunyu
Address:615 Michael Street, Atlanta, GA, 30322, USA
Email:chunyu.ma@emory.edu
Phone:(404) 727 5091
Funding Source:NIEHS ES026560
Contributors:Benjamin Kopp, MD

Subject:

Subject ID:SU001166
Subject Type:Plasma samples
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:4 months - 10 years

Factors:

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

mb_sample_id local_sample_id INFANT? 1=YES 0=CHILD Smoke exposure? 1=Yes 0=No CF? 1=Yes 0=No Gender
SA0767087_Baseline_21 1 1 F
SA07670943_Baseline_11 1 1 F
SA07671072_Baseline_21 1 1 F
SA07671171_Baseline_11 1 1 F
SA0767127_Baseline_11 1 1 F
SA07671374_Baseline_11 1 1 F
SA07671472_Baseline_11 1 1 F
SA07671573_Baseline_11 1 1 F
SA07671673_Baseline_21 1 1 F
SA07671771_Baseline_21 1 1 F
SA07671879_Baseline_21 1 1 F
SA07671979_Baseline_11 1 1 F
SA07672074_Baseline_21 1 1 F
SA07672143_Baseline_21 1 1 F
SA07672236_Baseline_21 1 1 M
SA07672378_Baseline_11 1 1 M
SA0767244_Baseline_21 1 1 M
SA0767254_Baseline_11 1 1 M
SA0767269_Baseline_11 1 1 M
SA07672778_Baseline_21 1 1 M
SA076728NCH_002_21 1 1 M
SA07672936_Baseline_11 1 1 M
SA076730NCH_002_11 1 1 M
SA076731ncH_001_11 1 1 M
SA076732ncH_001_21 1 1 M
SA0767339_Baseline_21 1 1 M
SA07668615_Baseline_11 - 1 F
SA0766878_Baseline_21 - 1 F
SA07668815_Baseline_21 - 1 F
SA0766895_Baseline_11 - 1 F
SA07669080_Baseline_11 - 1 F
SA0766918_Baseline_11 - 1 F
SA07669235_Baseline_21 - 1 F
SA07669380_Baseline_21 - 1 F
SA07669435_Baseline_11 - 1 F
SA0766955_Baseline_21 - 1 F
SA07669675_Baseline_21 - 1 M
SA0766976_Baseline_21 - 1 M
SA07669876_Baseline_21 - 1 M
SA07669910_Baseline_21 - 1 M
SA07670038_Baseline_11 - 1 M
SA0767016_Baseline_11 - 1 M
SA07670238_Baseline_21 - 1 M
SA07670376_Baseline_11 - 1 M
SA07670475_Baseline_11 - 1 M
SA07670567_Baseline_21 - 1 M
SA07670610_Baseline_11 - 1 M
SA07670767_Baseline_11 - 1 M
SA076672hc_60_21 - - F
SA076673hc_48_21 - - F
SA076674hc_48_11 - - F
SA076675hc_60_11 - - F
SA076676hc_12_11 - - M
SA076677hc_32_21 - - M
SA076678hc_32_11 - - M
SA076679NCH_003_21 - - M
SA076680hc_12_21 - - M
SA076681hc_30_21 - - M
SA076682hc_62_11 - - M
SA076683hc_30_11 - - M
SA076684NCH_003_11 - - M
SA076685hc_62_21 - - M
SA07663023_Visit_2_2- 1 1 F
SA07663151_Baseline_2- 1 1 F
SA07663261_Baseline_2- 1 1 F
SA07663365_Baseline_2- 1 1 F
SA07663468_Baseline_2- 1 1 F
SA07663549_Baseline_2- 1 1 F
SA07663643_Visit_2_2- 1 1 F
SA07663732_Baseline_2- 1 1 F
SA07663835_Visit_2_2- 1 1 F
SA07663929_Baseline_2- 1 1 F
SA07664014_Baseline_2- 1 1 F
SA07664132_Baseline_1- 1 1 F
SA07664214_Baseline_1- 1 1 F
SA07664323_Visit_2_1- 1 1 F
SA07664461_Baseline_1- 1 1 F
SA07664568_Baseline_1- 1 1 F
SA07664665_Baseline_1- 1 1 F
SA07664735_Visit_2_1- 1 1 F
SA07664829_Baseline_1- 1 1 F
SA07664951_Baseline_1- 1 1 F
SA07665049_Baseline_1- 1 1 F
SA07665143_Visit_2_1- 1 1 F
SA07665242_Baseline_1- 1 1 M
SA07665364_Baseline_1- 1 1 M
SA07665437_Baseline_1- 1 1 M
SA07665555_Baseline_2- 1 1 M
SA07665642_Baseline_2- 1 1 M
SA07665745_Baseline_2- 1 1 M
SA07665810_Visit_2_1- 1 1 M
SA07665963_Baseline_2- 1 1 M
SA07666063_Baseline_1- 1 1 M
SA07666130_Baseline_1- 1 1 M
SA07666231_Baseline_1- 1 1 M
SA07666345_Baseline_1- 1 1 M
SA07666437_Baseline_2- 1 1 M
SA07666555_Baseline_1- 1 1 M
SA07666654_Baseline_1- 1 1 M
SA07666764_Baseline_2- 1 1 M
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Collection:

Collection ID:CO001160
Collection Summary:Children ages 3 months to <10 years with CF were recruited from outpatient CF clinics, and stratified according to age (infants <1 year, and children 1-10 years).The diagnosis of CF was defined by two disease-causing mutations or a sweat chloride test = 60 mmol/L. The study was approved by the Institutional Review Board at Nationwide Childrens Hospital (IRB 12-00084). A parent or guardian of the child participant provided informed consent on their behalf. Healthy, non-CF age-matched controls were recruited from primary care clinics. For each participant, plasma was collected during a state of baseline, non-fasting health as infants would not be able to fast for collection. Plasma was immediately flash frozen at -80C for metabolite preservation.
Sample Type:Serum
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001180
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:SP001173
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_sample_preparation_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 AN001761 AN001762
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 area Peak Area

Chromatography:

Chromatography ID:CH001286
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 Amide (50 x 2.1mm, 2.5um)
Column Temperature:60C
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:CH001287
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 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:MS001679
Analysis ID:AN001761
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:None
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
Scanning Range:85-1275
  
MS ID:MS001680
Analysis ID:AN001762
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:None
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
Scanning Range:85-1275
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