Summary of Study ST001200

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 PR000808. The data can be accessed directly via it's Project DOI: 10.21228/M87M3D 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001200
Study TitleBiological Responses to Tobacco Smoke Exposure in III Children: Inflammatory Processes and the Oral Microbiome
Study SummaryThis project evaluates the biological response to overall tobacco smoke (OTS) exposure among pediatric emergency patients enrolled in a randomized-controlled intervention trial aimed at reducing secondhand smoke exposure. The effects of OTS as measured by salivary continine on salivary metabolic profiles are measured by untargeted high resolution metabolomics, comparing higher and lower levels of OTS.
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameUppal
First NameKaran
AddressNA
Emailkuppal2@emory.edu
Phone(404) 727 5027
Submit Date2019-06-12
Total Subjects284
Study CommentsBoth CHEAR pooled saliva samples and Clinical Biomarker Laboratory pooled plasma samples were used
Raw Data AvailableYes
Raw Data File Type(s)mzXML, raw(Thermo)
Chear Study2017-1762
Analysis Type DetailLC-MS
Release Date2020-05-11
Release Version1
Karan Uppal Karan Uppal
https://dx.doi.org/10.21228/M87M3D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000808
Project DOI:doi: 10.21228/M87M3D
Project Title:Biological Responses to Tobacco Smoke Exposure in III Children: Inflammatory Processes and the Oral Microbiome
Project Type:NIH/NIEHS 1U2CES026560-01
Project Summary:This project evaluates the biological response to overall tobacco smoke (OTS) exposure among pediatric emergency patients enrolled in a randomized-controlled intervention trial aimed at reducing secondhand smoke exposure. The effects of OTS as measured by salivary continine on salivary metabolic profiles are measured by untargeted high resolution metabolomics, comparing higher and lower levels of OTS.
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Tran
First Name:ViLinh
Address:NA
Email:vtran6@emory.edu
Phone:(404) 727 5027
Funding Source:NIEHS ES026560

Subject:

Subject ID:SU001267
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Ages 0 to 17 years

Factors:

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

mb_sample_id local_sample_id Plasma
SA083514Q-Std Plasma pool_5c_1Plasma
SA083515Q-Std Plasma pool_3e_1Plasma
SA083516Q-Std Plasma pool_5d_1Plasma
SA083517Q-Std Plasma pool_7b_1Plasma
SA083518Q-Std Plasma pool_7a_1Plasma
SA083519Q-Std Plasma pool_2a_1Plasma
SA083520Q-Std Plasma pool_6f_1Plasma
SA083521Q-Std Plasma pool_3f_1Plasma
SA083522Q-Std Plasma pool_4b_1Plasma
SA083523Q-Std Plasma pool_7c_1Plasma
SA083524Q-Std Plasma pool_4a_1Plasma
SA083525Q-Std Plasma pool_1e_1Plasma
SA083526Q-Std Plasma pool_1f_1Plasma
SA083527Q-Std Plasma pool_6e_1Plasma
SA083528Q-Std Plasma pool_2d_1Plasma
SA083529Q-Std Plasma pool_6b_1Plasma
SA083530Q-Std Plasma pool_6a_1Plasma
SA083531Q-Std Plasma pool_2e_1Plasma
SA083532Q-Std Plasma pool_2f_1Plasma
SA083533Q-Std Plasma pool_3b_1Plasma
SA083534Q-Std Plasma pool_3a_1Plasma
SA083535Q-Std Plasma pool_6c_1Plasma
SA083536Q-Std Plasma pool_6d_1Plasma
SA083537Q-Std Plasma pool_3d_1Plasma
SA083538Q-Std Plasma pool_7d_1Plasma
SA083539Q-Std Plasma pool_3c_1Plasma
SA083540Q-Std Plasma pool_5e_1Plasma
SA083541Q-Std Plasma pool_5f_1Plasma
SA083542Q-Std Plasma pool_2c_1Plasma
SA083543Q-Std Plasma pool_2b_1Plasma
SA083544Q-Std Plasma pool_5a_1Plasma
SA083545Q-Std Plasma pool_1c_1Plasma
SA083546Q-Std Plasma pool_1d_1Plasma
SA083547NIST SRM 1950_1aPlasma
SA083548Q-Std Plasma pool_4d_1Plasma
SA083549Q-Std Plasma pool_7f_1Plasma
SA083550Q-Std Plasma pool_7e_1Plasma
SA083551NIST SRM 1950_2aPlasma
SA083552Q-Std Plasma pool_4f_1Plasma
SA083553Q-Std Plasma pool_4c_1Plasma
SA083554Q-Std Plasma pool_5b_1Plasma
SA083555Q-Std Plasma pool_1a_1Plasma
SA083556Q-Std Plasma pool_1b_1Plasma
SA083557Q-Std Plasma pool_4e_1Plasma
SA083558C-1GNU8-SL-01_2Saliva
SA083559C-1GL68-SL-01_2Saliva
SA083560C-1GNV6-SL-01_2Saliva
SA083561C-1GNN3-SL-01_2Saliva
SA083562C-1GN82-SL-01_2Saliva
SA083563C-1GN74-SL-01_2Saliva
SA083564C-1GN90-SL-01_2Saliva
SA083565C-1GNE3-SL-01_2Saliva
SA083566C-1GNM6-SL-01_2Saliva
SA083567C-1GNL8-SL-01_2Saliva
SA083568C-1GL76-SL-01_2Saliva
SA083569salivapool_5e_1Saliva
SA083570C-1GPC6-SL-01_2Saliva
SA083571C-1GKX4-SL-01_2Saliva
SA083572C-1GP98-SL-01_2Saliva
SA083573C-1GPD3-SL-01_2Saliva
SA083574C-1GPG7-SL-01_2Saliva
SA083575C-1GPK8-SL-01_2Saliva
SA083576C-1GPJ0-SL-01_2Saliva
SA083577C-1GP64-SL-01_2Saliva
SA083578salivapool_6b_1Saliva
SA083579C-1GN41-SL-01_2Saliva
SA083580C-1GL27-SL-01_2Saliva
SA083581C-1GL35-SL-01_2Saliva
SA083582C-1GL19-SL-01_2Saliva
SA083583salivapool_5f_1Saliva
SA083584salivapool_6a_1Saliva
SA083585C-1GKY2-SL-01_2Saliva
SA083586C-1GP07-SL-01_2Saliva
SA083587C-1GN09-SL-01_2Saliva
SA083588C-SZJH5-SL-01_2Saliva
SA083589C-1GMD6-SL-01_2Saliva
SA083590C-1GMC9-SL-01_2Saliva
SA083591C-1GMH8-SL-01_2Saliva
SA083592C-1GMJ3-SL-01_2Saliva
SA083593C-1GL92-SL-01_2Saliva
SA083594C-1GLA4-SL-01_2Saliva
SA083595C-1GM91-SL-01_2Saliva
SA083596C-1GM67-SL-01_2Saliva
SA083597C-1GLF3-SL-01_2Saliva
SA083598C-1GLT2-SL-01_2Saliva
SA083599C-1GLS4-SL-01_2Saliva
SA083600C-1GLD7-SL-01_2Saliva
SA083601C-1GLV8-SL-01_2Saliva
SA083602C-1GLW6-SL-01_2Saliva
SA083603C-QDNY3-SL-01_2Saliva
SA083604C-1GMK1-SL-01_2Saliva
SA083605C-1GML9-SL-01_2Saliva
SA083606C-1GMV7-SL-01_2Saliva
SA083607salivapool_4e_1Saliva
SA083608salivapool_4f_1Saliva
SA083609C-1GMX2-SL-01_2Saliva
SA083610C-1GLG1-SL-01_2Saliva
SA083611C-1GN25-SL-01_2Saliva
SA083612C-1GN17-SL-01_2Saliva
SA083613C-1GMR6-SL-01_2Saliva
Showing page 1 of 4     Results:    1  2  3  4  Next     Showing results 1 to 100 of 364

Collection:

Collection ID:CO001261
Collection Summary:Saliva samples were collected from participants in the randomized controlled trial, An Intervention to Reduce Secondhand Smoke Exposure among Pediatric Emergency Patients, at baseline and a six-week follow up visit. Saliva samples were collected at baseline and a six-week follow up visit by standard protocol using oral swab collection, centrifugation and aliquots trasnferred to 1.8ml freezer tubes and stored in a -70 degree C freezer. The samples were shipped on dry ice from the Cincinnati Children's Hospital Medical Center biorepository storage facility and subsequently to the metabolomics analysis lab at Emory University.
Sample Type:plasma
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001282
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:SP001275
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 AN001996 AN001997
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 column. 2.1mm x 50mm x 2.5μm particle size with Thermo Accucore HILIC guard column Higgins endcapped C18 stainless steel column. 2.1mm x 50mm x 3μm particle size, Product #TS-0521-C183; Thermo Accucore C18 guard column 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:CH001444
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 column. 2.1mm x 50mm x 2.5μm particle size with Thermo Accucore HILIC guard column
Column Temperature:60 C
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:CH001445
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
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Higgins endcapped C18 stainless steel column. 2.1mm x 50mm x 3μm particle size, Product #TS-0521-C183; Thermo Accucore C18 guard column with holder, Product #17126-014005
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:MS001849
Analysis ID:AN001996
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:NA
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
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
  
MS ID:MS001850
Analysis ID:AN001997
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:NA
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
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
  logo