Summary of Study ST001262

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 PR000847. The data can be accessed directly via it's Project DOI: 10.21228/M86H4F 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 IDST001262
Study TitleThe impact of tobacco smoke exposure and environmental exposures on the pulmonary microbiome of critically ill children
Study SummaryThis project evaluates the effects of tobacco smoke exposure (TSE) on the pediatric lung microbiome in critically ill children. The impact of TSE on the airway microbiome of critically ill, mechanically ventilated pediatric patients will be determined by through clinical outcomes and analysis of urinary and plasma metabolomes to identify other environmental exposures contributing to the alteration of the pediatric microbiome.
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameUppal
First NameKaran
AddressNA
Emailkuppal2@emory.edu
Phone(404) 727 5027
Submit Date2019-06-25
Total Subjects367
Study CommentsBoth CHEAR pooled urine samples and Clinical Biomarker Laboratory pooled plasma samples were used
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/M86H4F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000847
Project DOI:doi: 10.21228/M86H4F
Project Title:The impact of tobacco smoke exposure and environmental exposures on the pulmonary microbiome of critically ill children
Project Type:NIH/NIEHS 1U2CES026560-01
Project Summary:This project evaluates the effects of tobacco smoke exposure (TSE) on the pediatric lung microbiome in critically ill children. The impact of TSE on the airway microbiome of critically ill, mechanically ventilated pediatric patients will be determined by through clinical outcomes and analysis of urinary and plasma metabolomes to identify other environmental exposures contributing to the alteration of the pediatric microbiome.
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:SU001330
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:31 d to 18 yr

Factors:

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

mb_sample_id local_sample_id plasma
SA091515Q-Std Plasma pool_4b_1plasma
SA091516Q-Std Plasma pool_8a_1plasma
SA091517Q-Std Plasma pool_5a_1plasma
SA091518Q-Std Plasma pool_7a_1plasma
SA091519Q-Std Plasma pool_6a_1plasma
SA091520Q-Std Plasma pool_2b_1plasma
SA091521Q-Std Plasma pool_5b_1plasma
SA091522Q-Std Plasma pool_6b_1plasma
SA091523Q-Std Plasma pool_8b_1plasma
SA091524Q-Std Plasma pool_2a_1plasma
SA091525chearurine_2d_1plasma
SA091526chearurine_2c_1plasma
SA091527Q-Std Plasma pool_1b_1plasma
SA091528Q-Std Plasma pool_4a_1plasma
SA091529Q-Std Plasma pool_3a_1plasma
SA091530Q-Std Plasma pool_3b_1plasma
SA091531Q-Std Plasma pool_9a_1plasma
SA091532Q-Std Plasma pool_7b_1plasma
SA091533Q-Std Plasma pool_1a_1plasma
SA091534NIST SRM 1950_1bplasma
SA091535NIST SRM 1950_1aplasma
SA091536Q-Std Plasma pool_9b_1plasma
SA091537C-1PVB2-U-00_1urine
SA091538C-1PRT6-U-00_1urine
SA091539C-1PVE5-U-00_1urine
SA091540C-1PVJ4-U-00_1urine
SA091541chearurine_7c_1urine
SA091542chearurine_7d_1urine
SA091543chearurine_6f_1urine
SA091544chearurine_6e_1urine
SA091545C-1PV01-U-00_1urine
SA091546C-1PUQ0-U-00_1urine
SA091547C-1PT86-U-00_1urine
SA091548C-1PT37-U-00_1urine
SA091549C-1PT29-U-00_1urine
SA091550C-1PSR0-U-00_1urine
SA091551C-1PT94-U-00_1urine
SA091552C-1PTQ1-U-00_1urine
SA091553C-1PQW1-U-00_1urine
SA091554C-1PU69-U-00_1urine
SA091555C-1PU36-U-00_1urine
SA091556C-1PUU1-U-00_1urine
SA091557C-1PQL5-U-00_1urine
SA091558C-1PWP0-U-00_1urine
SA091559C-1PWB1-U-00_1urine
SA091560C-1PZA0-U-00_1urine
SA091561C-1PZB8-U-00_1urine
SA091562C-1PZ64-U-00_1urine
SA091563C-1PYS1-U-00_1urine
SA091564C-1PY99-U-00_1urine
SA091565C-1PXM6-U-00_1urine
SA091566C-1PX90-U-00_1urine
SA091567C-1PWQ8-U-00_1urine
SA091568C-1PZE1-U-00_1urine
SA091569C-1PQ06-U-00_1urine
SA091570C-1PVM8-U-00_1urine
SA091571chearurine_7b_1urine
SA091572chearurine_7a_1urine
SA091573C-1PQH4-U-00_1urine
SA091574C-1PW26-U-00_1urine
SA091575C-1PW34-U-00_1urine
SA091576C-1PS38-U-00_1urine
SA091577C-1PQA9-U-00_1urine
SA091578C-1PW42-U-00_1urine
SA091579C-1PYA1-U-00_1urine
SA091580chearurine_6c_1urine
SA091581C-1PUN6-U-00_1urine
SA091582C-1PV92-U-00_1urine
SA091583C-1PUH0-U-00_1urine
SA091584C-1PUD8-U-00_1urine
SA091585C-1PU44-U-00_1urine
SA091586C-1PVG1-U-00_1urine
SA091587C-1PVH9-U-00_1urine
SA091588chearurine_6b_1urine
SA091589C-1PVT2-U-00_1urine
SA091590chearurine_6a_1urine
SA091591chearurine_5f_1urine
SA091592chearurine_5e_1urine
SA091593C-1PU28-U-00_1urine
SA091594C-1PTJ6-U-00_1urine
SA091595C-1PRL4-U-00_1urine
SA091596C-1PRS8-U-00_1urine
SA091597C-1PRJ8-U-00_1urine
SA091598C-1PR54-U-00_1urine
SA091599C-1PQT7-U-00_1urine
SA091600C-1PSA7-U-00_1urine
SA091601C-1PSB5-U-00_1urine
SA091602C-1PSN8-U-00_1urine
SA091603C-1PSJ7-U-00_1urine
SA091604C-1PSG4-U-00_1urine
SA091605C-1PSE8-U-00_1urine
SA091606C-1PW18-U-00_1urine
SA091607C-1PW75-U-00_1urine
SA091608C-1PQD2-U-00_1urine
SA091609C-1PQR2-U-00_1urine
SA091610C-1PQ55-U-00_1urine
SA091611C-1PZW2-U-00_1urine
SA091612C-1PZU6-U-00_1urine
SA091613C-1PRW0-U-00_1urine
SA091614chearurine_6d_1urine
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Collection:

Collection ID:CO001324
Collection Summary:Urine samples were collected from participants in the longitudinal study, Microbiome, Virome and Host Responses Preceding Ventilator-Associated Pneumonia, as a single specimen collection following intubation. Urine samples were collected non-invasively from indwelling Foley catheters, bed pans or other urine receptacles. Aliquots of urine were transferred to 1.8mL freezer tubes and stores in a -70C freezer. The samples were shipped on dry ice from the University of Colorado Denver biorepository and subsequently to the metabolomics analysis lab at Emory University.
Sample Type:Urine
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001345
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:SP001338
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 AN002094 AN002095
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Dionex UltiMate 3000 Dionex UltiMate 3000
Column Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 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:CH001529
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:Dionex UltiMate 3000
Column Name:Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard
Column Temperature:60C
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:CH001530
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: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 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:MS001945
Analysis ID:AN002094
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:MS001946
Analysis ID:AN002095
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
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