Summary of Study ST001800

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 PR001136. The data can be accessed directly via it's Project DOI: 10.21228/M8VQ4D 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 IDST001800
Study TitleCHDWB human plasma exposomics analysis - 2
Study TypeUntargeted MS anlaysis
Study SummaryWe analyzed 80 archival samples from individuals (57 females, 23 males; aged 41 to 68 y) without known disease or occupational or environmental exposures of concern as a pilot to test the utility of XLE in large-scale human biomonitoring studies. Using a requirement for at least 3 co-eluting accurate mass m/z features ( 5 ppm) within 30 s of database retention time, we identified 49 chemicals belonging to various environmental chemical classes. An unsupervised 2-way hierarchical cluster analysis (HCA) of log transformed intensity showed clustering according to chemical class. In particular, persistent chemicals were highly correlated with each other (all raw P < 0.001), including p,p’-DDE, PCBs 153, 180, 138, 118 and 74, PBDE-47, hexachlorobenzene (HCB) and trans-nonachlor. Results showed a general increase of chemical levels with increasing age quartiles (Q3 and Q4 : 53 to 68 versus Q1 and Q2: 41 to 52) using unsupervised clustering, a trend particularly evident for the cluster of p,p’-DDE, PCBs 153, 180, 138, 118 and 74, PBDE-47, HCB and trans-nonachlor. Examination of data according to body mass index (BMI) showed that individuals with BMI ≥ 40 had lower levels of environmental chemicals, which may be attributed to high lipophilicity and propensity to distribute in adipose tissue versus plasma. Quantification with reference standardization showed that use of two SRM samples with differing environmental chemical concentrations can overcome variable batch effects in quantification for large-scale studies. Examples of the most frequently detected chemicals shows that overall distributions were positively skewed by a small subset of individuals with high concentrations.
Institute
Emory University
DepartmentMedicine/Pulmonary
LaboratoryDean Jones
Last NameHu
First NameXin
AddressEmory University Whitehead building (Rm 225), 615 Michael Street
Emailxin.hu2@emory.edu
Phone4047275091
Submit Date2021-05-06
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailGC-MS
Release Date2021-05-28
Release Version1
Xin Hu Xin Hu
https://dx.doi.org/10.21228/M8VQ4D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001136
Project DOI:doi: 10.21228/M8VQ4D
Project Title:A scalable workflow for the human exposome
Project Type:Untargeted GC-MS quantitative analysis
Project Summary:Complementing the genome with an understanding of the human exposome is an important challenge for contemporary science and technology. Tens of thousands of chemicals are used in commerce, yet cost for targeted environmental chemical analysis limits surveillance to a few hundred known hazards. To overcome limitations which prevent scaling to thousands of chemicals, we developed a single-step express liquid extraction (XLE), gas chromatography high-resolution mass spectrometry (GC-HRMS) analysis and computational pipeline to operationalize the human exposome. We show that the workflow supports quantification of environmental chemicals in human plasma (200 µL) and tissue (≤ 100 mg) samples. The method also provides high resolution, sensitivity and selectivity for exposome epidemiology of mass spectral features without a priori knowledge of chemical identity. The simplicity of the method can facilitate harmonization of environmental biomonitoring between laboratories and enable population level human exposome research with limited sample volume.
Institute:Emory University
Department:Medicine, Pulmonary
Laboratory:Dean Jones
Last Name:Hu
First Name:Xin
Address:Emory University Whitehead building (Rm 225), 615 Michael Street, Atlanta, Georgia, 30322, USA
Email:xin.hu2@emory.edu
Phone:4047275091
Funding Source:This study was supported by the NIEHS, U2C ES030163 (DPJ), U2C ES030859 (DIW) and P30 ES019776 (CJM), NIDDK RC2 DK118619 (KNL), NHLBI R01 HL086773 (DPJ), US Department of Defense W81XWH2010103 (DPJ), and the Chris M. Carlos and Catharine Nicole Jockisch Carlos Endowment Fund in Primary Sclerosing Cholangitis (PSC) (KNL).
Contributors:Xin Hu, Douglas I. Walker, Yongliang Liang, M. Ryan Smith, Michael L. Orr, Brian D. Juran, Chunyu Ma, Karan Uppal, Michael Koval, Greg S. Martin, David C. Neujahr, Carmen J. Marsit, Young-Mi Go, Kurt Pennell, Gary W. Miller, Konstantinos N. Lazaridis, Dean P. Jones

Subject:

Subject ID:SU001877
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id type
SA167269BL_200220_M393_604Plasma
SA167270BL_200220_M393_603Plasma
SA167271BL_200220_M393_602Plasma
SA167272BL_200220_M393_605Plasma
SA167273BL_200220_M393_606Plasma
SA167274BL_200220_M393_608Plasma
SA167275BL_200220_M393_607Plasma
SA167276BL_200220_M393_601Plasma
SA167277BL_200220_M393_600Plasma
SA167278BL_200220_M393_595Plasma
SA167279BL_200220_M393_594Plasma
SA167280BL_200220_M393_596Plasma
SA167281BL_200220_M393_597Plasma
SA167282BL_200220_M393_599Plasma
SA167283BL_200220_M393_598Plasma
SA167284BL_200220_M393_609Plasma
SA167285BL_200220_M393_610Plasma
SA167286BL_200220_M393_620Plasma
SA167287BL_200220_M393_619Plasma
SA167288BL_200220_M393_621Plasma
SA167289BL_200220_M393_622Plasma
SA167290BL_200220_M393_624Plasma
SA167291BL_200220_M393_623Plasma
SA167292BL_200220_M393_618Plasma
SA167293BL_200220_M393_617Plasma
SA167294BL_200220_M393_612Plasma
SA167295BL_200220_M393_611Plasma
SA167296BL_200220_M393_613Plasma
SA167297BL_200220_M393_614Plasma
SA167298BL_200220_M393_616Plasma
SA167299BL_200220_M393_615Plasma
SA167300BL_200220_M393_593Plasma
SA167301BL_200220_M393_592Plasma
SA167302BL_200220_M393_573Plasma
SA167303BL_200220_M393_572Plasma
SA167304BL_200220_M393_574Plasma
SA167305BL_200220_M393_575Plasma
SA167306BL_200220_M393_577Plasma
SA167307BL_200220_M393_571Plasma
SA167308BL_200220_M393_570Plasma
SA167309BL_200220_M393_566Plasma
SA167310BL_200220_M393_565Plasma
SA167311BL_200220_M393_567Plasma
SA167312BL_200220_M393_568Plasma
SA167313BL_200220_M393_569Plasma
SA167314BL_200220_M393_578Plasma
SA167315BL_200220_M393_576Plasma
SA167316BL_200220_M393_579Plasma
SA167317BL_200220_M393_586Plasma
SA167318BL_200220_M393_588Plasma
SA167319BL_200220_M393_589Plasma
SA167320BL_200220_M393_591Plasma
SA167321BL_200220_M393_590Plasma
SA167322BL_200220_M393_585Plasma
SA167323BL_200220_M393_587Plasma
SA167324BL_200220_M393_584Plasma
SA167325BL_200220_M393_581Plasma
SA167326BL_200220_M393_580Plasma
SA167327BL_200220_M393_582Plasma
SA167328BL_200220_M393_583Plasma
SA167329BL_200220_M393_560SRM1957
SA167330BL_200220_M393_559SRM1957
SA167331BL_200220_M393_561SRM1957
SA167332BL_200220_M393_564SRM1958
SA167333BL_200220_M393_563SRM1958
SA167334BL_200220_M393_562SRM1958
Showing results 1 to 66 of 66

Collection:

Collection ID:CO001870
Collection Summary:200 µL ethylenediaminetetraacetic acid (EDTA)-treated plasma samples were collected following standard operating procedures from 80 individuals without known disease and were randomly selected from archival samples obtained from the Center for Health Discovery and Well Being (CHDWB) cohort of approximately 750 individuals. The original study was conducted under Emory Investigational Review Board (IRB approval No. 00007243) and included both genders and individuals self-identifying as white, black, Hispanic and Asian. SRM-1957 and SRM-1958 were obtained from National Institute of Standard and Technology (NIST) as quality control and assurance measures run in parallel to study samples.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001890
Treatment Summary:50 µL formic acid (Emprove® Essential DAC, Sigma-Aldrich) was added to 200 µL SRM aliquots and immediately followed by addition of 200 µL hexane – ethyl acetate (2:1 v/v, ≥99% pure, Sigma-Aldrich) containing the internal standards (final concentration: 1 ng/mL). The sample mixture was shaken vigorously on ice using multi-tube vortexer (VWR VX-2500) for 1 h and centrifuged at 1000 g, 4 °C for 10 min. The sample mixture was chilled during entire extraction procedure. The organic supernatant was transferred to a new tube with 25 mg MgSO4 (≥99.99% pure, Sigma-Aldrich) and vortexed vigorously to remove water. After 10 min centrifugation at 1000 g, 80 µL of the final supernatant was spiked with instrumental internal standards (final concentration: 1 ng/mL) for analysis. Two 13C labeled chemicals [13C12]PCB-28 and [13C12]PBB-153 were used as volumetric internal standards added to the final extract, and nine 13C labeled chemicals (99% isotope enrichment for each) were spiked as recovery standards to estimate chemical recovery efficiency by XLE: [13C12]PCB-101, [13C12]PCB-153, [13C12]PCB-180, [13C12]PBDE-47, [13C12]PBDE-99, [13C6]anthracene, [13C10]mirex, [13C6]cis-permethrin, and [13C12]p,p’-DDE.

Sample Preparation:

Sampleprep ID:SP001883
Sampleprep Summary:Same as treatment

Combined analysis:

Analysis ID AN002922
Analysis type MS
Chromatography type GC
Chromatography system Thermo Trace 1310
Column Agilent DB5-MS (15m x 0.25mm,0.25um)
MS Type EI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units raw intensity

Chromatography:

Chromatography ID:CH002164
Chromatography Summary:Samples were analyzed with three injections using GC-HRMS with a Thermo Scientific Q Exactive GC hybrid quadrupole Orbitrap mass spectrometer with 2 µL per injection. A capillary DB-5MS column (15 m × 0.25 mm × 0.25 µm film thickness) was used with the following temperature program: hold 75 °C for 1 min, 25 °C/min to 180 °C, 6 °C/min to 250 °C, 20 °C/min to 350 °C and hold for 5 min. The flow rate of the helium carrier gas was 1 mL/min. Ion source and transfer line temperatures were 250°C and 280°C, respectively. Data were collected from 3 to 24.37 min with positive electron ionization (EI) mode (+70 eV), scanning from m/z 85.0000 to 850.0000 with a resolution of 60,000.
Instrument Name:Thermo Trace 1310
Column Name:Agilent DB5-MS (15m x 0.25mm,0.25um)
Chromatography Type:GC

MS:

MS ID:MS002714
Analysis ID:AN002922
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:EI
MS Comments:Data were collected from 3 to 24.37 min with positive electron ionization (EI) mode (+70 eV), scanning from m/z 85.0000 to 850.0000 with a resolution of 60,000. Raw data were examined by checking signal-to-noise ratio, peak shape and spectral information for surrogate and internal standards using a 5 ppm m/z tolerance and 30 s retention time window in xCalibur Qualbrowser software. Data extraction was performed by XCMS to generate about 40,000 chemical features identified by spectral m/z and retention time.
Ion Mode:POSITIVE
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