Summary of Study ST001335

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 PR000912. The data can be accessed directly via it's Project DOI: 10.21228/M8T112 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 IDST001335
Study TitleAir Pollution, Placenta Function, and Birth Outcomes in Los Angeles in the Placental Assessment in Response to ENvironmenTal pollution study (PARENTs) cohort
Study SummaryThis project aims to evaluate the internal environmental exposome of mother/fetus pairs within the PARENTs cohort, assessing a wide range of biomarkers/internal exposure measures for environmental toxins including air pollutants. Focusing on advanced imaging data on placental development and robust, clinically-confirmed birth outcomes, this a hypothesis-generating, untargeted pilot metabolomics study aims to identify potential predictors of placental insufficiencies and adverse birth outcomes. Measurements of exposures which include residential, occupational, and behavioral exposures, along with personalized air pollution measures, will help us in identifying related metabolomics patterns.
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 Date2020-02-20
Total Subjects440
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2022-09-27
Release Version1
Karan Uppal Karan Uppal
https://dx.doi.org/10.21228/M8T112
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000912
Project DOI:doi: 10.21228/M8T112
Project Title:Air Pollution, Placenta Function, and Birth Outcomes in Los Angeles in the Placental Assessment in Response to ENvironmenTal pollution study (PARENTs) cohort
Project Type:NIH/NIEHS U2CES025660
Project Summary:This project aims to evaluate the internal environmental exposome of mother/fetus pairs within the PARENTs cohort, assessing a wide range of biomarkers/internal exposure measures for environmental toxins including air pollutants. Focusing on advanced imaging data on placental development and robust, clinically-confirmed birth outcomes, this a hypothesis-generating, untargeted pilot metabolomics study aims to identify potential predictors of placental insufficiencies and adverse birth outcomes. Measurements of exposures which include residential, occupational, and behavioral exposures, along with personalized air pollution measures, will help us in identifying related metabolomics patterns.
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Uppal
First Name:Karan
Address:615 Michael Street, Atlanta, GA, 30322, USA
Email:kuppal2@emory.edu
Phone:(404) 727 5027
Funding Source:NIH/NIEHS : U2CES025660
Contributors:Beate Ritz, MD, PhD Sherin Devaskar, MD Dean P. Jones, PhD

Subject:

Subject ID:SU001409
Subject Type:Serum samples
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:Adult pregnant women - age 18 years and older, Infants: Age 0 to 3 months of age
Gender:Female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Plasma
SA096805chearplasma_5f_2Plasma
SA096806q3June2014_5b_2Plasma
SA096807q3June2014_6a_2Plasma
SA096808chearplasma_5e_2Plasma
SA096809chearplasma_5c_2Plasma
SA096810chearplasma_5a_2Plasma
SA096811chearplasma_5b_2Plasma
SA096812chearplasma_6a_2Plasma
SA096813chearplasma_5d_2Plasma
SA096814chearplasma_6c_2Plasma
SA096815q3June2014_7a_2Plasma
SA096816chearplasma_7a_2Plasma
SA096817chearplasma_7b_2Plasma
SA096818q3June2014_6b_2Plasma
SA096819chearplasma_6f_2Plasma
SA096820q3June2014_5a_2Plasma
SA096821nist1_2Plasma
SA096822chearplasma_6e_2Plasma
SA096823chearplasma_6b_2Plasma
SA096824q3June2014_4b_2Plasma
SA096825chearplasma_3c_2Plasma
SA096826chearplasma_3d_2Plasma
SA096827chearplasma_3e_2Plasma
SA096828chearplasma_3b_2Plasma
SA096829chearplasma_3a_2Plasma
SA096830chearplasma_2f_2Plasma
SA096831q3June2014_2a_2Plasma
SA096832q3June2014_3a_2Plasma
SA096833chearplasma_3f_2Plasma
SA096834q3June2014_3b_2Plasma
SA096835chearplasma_4d_2Plasma
SA096836chearplasma_4e_2Plasma
SA096837chearplasma_4f_2Plasma
SA096838chearplasma_4c_2Plasma
SA096839chearplasma_4b_2Plasma
SA096840q3June2014_4a_2Plasma
SA096841chearplasma_4a_2Plasma
SA096842chearplasma_7c_2Plasma
SA096843chearplasma_7d_2Plasma
SA096844chearplasma_10e_2Plasma
SA096845chearplasma_10f_2Plasma
SA096846q3June2014_10b_2Plasma
SA096847chearplasma_10d_2Plasma
SA096848chearplasma_10c_2Plasma
SA096849q3June2014_10a_2Plasma
SA096850chearplasma_10a_2Plasma
SA096851chearplasma_10b_2Plasma
SA096852q3June2014_11a_2Plasma
SA096853chearplasma_11a_2Plasma
SA096854chearplasma_11f_2Plasma
SA096855q3June2014_11b_2Plasma
SA096856nist2_2Plasma
SA096857chearplasma_11e_2Plasma
SA096858chearplasma_11d_2Plasma
SA096859chearplasma_11b_2Plasma
SA096860chearplasma_11c_2Plasma
SA096861q3June2014_9b_2Plasma
SA096862chearplasma_9f_2Plasma
SA096863chearplasma_8b_2Plasma
SA096864chearplasma_8c_2Plasma
SA096865chearplasma_8d_2Plasma
SA096866chearplasma_8a_2Plasma
SA096867q3June2014_8a_2Plasma
SA096868chearplasma_7e_2Plasma
SA096869chearplasma_7f_2Plasma
SA096870q3June2014_7b_2Plasma
SA096871chearplasma_8e_2Plasma
SA096872chearplasma_8f_2Plasma
SA096873chearplasma_9c_2Plasma
SA096874chearplasma_9d_2Plasma
SA096875chearplasma_9e_2Plasma
SA096876chearplasma_9b_2Plasma
SA096877chearplasma_9a_2Plasma
SA096878q3June2014_8b_2Plasma
SA096879q3June2014_9a_2Plasma
SA096880chearplasma_2e_2Plasma
SA096881chearplasma_6d_2Plasma
SA096882chearplasma_2b_2Plasma
SA096883chearplasma_2a_2Plasma
SA096884q3June2014_2b_2Plasma
SA096885chearplasma_1d_2Plasma
SA096886chearplasma_1e_2Plasma
SA096887chearplasma_1c_2Plasma
SA096888chearplasma_2c_2Plasma
SA096889chearplasma_2d_2Plasma
SA096890q3June2014_1b_2Plasma
SA096891chearplasma_1f_2Plasma
SA096892q3June2014_1a_2Plasma
SA096893chearplasma_1b_2Plasma
SA096894chearplasma_1a_2Plasma
SA096895C-1YWR6-S-00_2Serum
SA096896C-1YWQ8-S-00_2Serum
SA096897C-1YWP0-S-00_2Serum
SA096898C-1YWN4-S-00_2Serum
SA096899C-1YMR6-S-00_2Serum
SA096900C-1YMQ8-S-00_2Serum
SA096901C-1YWE4-S-00_2Serum
SA096902C-1YMN4-S-00_2Serum
SA096903C-1YMP0-S-00_2Serum
SA096904C-1YWM7-S-00_2Serum
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Collection:

Collection ID:CO001404
Collection Summary:Plasma and serum obtained from blood vein draw for pregnant mothers at first, second, third trimester and time of delivery or from cord blood sampling for infants at delivery in the PARENTs cohort. Plasma 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�C freezer. The samples were shipped on dry ice from the clinical centers to the CHEAR URR at Emory University.
Sample Type:Blood (serum)
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR001424
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:SP001417
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 AN002224 AN002225
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Dionex UltiMate 3000 Dionex UltiMate 3000
Column Waters XBridge BEH Amide XP (50 x 2.1mm,2.5um) with Thermo Accucore HILIC guard 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:CH001632
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
EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Dionex UltiMate 3000
Column Name:Waters XBridge BEH Amide XP (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 mi
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:CH001633
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 mmobile 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
EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Instrument Name: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:MS002070
Analysis ID:AN002224
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
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
  
MS ID:MS002071
Analysis ID:AN002225
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
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
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