Summary of Study ST001801

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 IDST001801
Study TitleCHDWB human plasma exposomics analysis - 1
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:SU001878
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
SA167335ExStd5_1External std
SA167336ExStd5_3External std
SA167337ExStd5_2External std
SA167338ExStd5_4External std
SA167339ExStd5_5External std
SA167340BL_200220_M393_311Plasma
SA167341BL_200220_M393_312Plasma
SA167342BL_200220_M393_332Plasma
SA167343BL_200220_M393_310Plasma
SA167344BL_200220_M393_331Plasma
SA167345BL_200220_M393_306Plasma
SA167346BL_200220_M393_305Plasma
SA167347BL_200220_M393_333Plasma
SA167348BL_200220_M393_307Plasma
SA167349BL_200220_M393_308Plasma
SA167350BL_200220_M393_309Plasma
SA167351BL_200220_M393_337Plasma
SA167352BL_200220_M393_341Plasma
SA167353BL_200220_M393_342Plasma
SA167354BL_200220_M393_343Plasma
SA167355BL_200220_M393_344Plasma
SA167356BL_200220_M393_340Plasma
SA167357BL_200220_M393_339Plasma
SA167358BL_200220_M393_335Plasma
SA167359BL_200220_M393_336Plasma
SA167360BL_200220_M393_304Plasma
SA167361BL_200220_M393_338Plasma
SA167362BL_200220_M393_334Plasma
SA167363BL_200220_M393_300Plasma
SA167364BL_200220_M393_288Plasma
SA167365BL_200220_M393_289Plasma
SA167366BL_200220_M393_290Plasma
SA167367BL_200220_M393_291Plasma
SA167368BL_200220_M393_287Plasma
SA167369BL_200220_M393_286Plasma
SA167370BL_200220_M393_281Plasma
SA167371BL_200220_M393_283Plasma
SA167372BL_200220_M393_284Plasma
SA167373BL_200220_M393_285Plasma
SA167374BL_200220_M393_292Plasma
SA167375BL_200220_M393_293Plasma
SA167376BL_200220_M393_299Plasma
SA167377BL_200220_M393_345Plasma
SA167378BL_200220_M393_301Plasma
SA167379BL_200220_M393_302Plasma
SA167380BL_200220_M393_298Plasma
SA167381BL_200220_M393_297Plasma
SA167382BL_200220_M393_294Plasma
SA167383BL_200220_M393_295Plasma
SA167384BL_200220_M393_296Plasma
SA167385BL_200220_M393_303Plasma
SA167386BL_200220_M393_349Plasma
SA167387BL_200220_M393_376Plasma
SA167388BL_200220_M393_377Plasma
SA167389BL_200220_M393_378Plasma
SA167390BL_200220_M393_379Plasma
SA167391BL_200220_M393_375Plasma
SA167392BL_200220_M393_374Plasma
SA167393BL_200220_M393_370Plasma
SA167394BL_200220_M393_371Plasma
SA167395BL_200220_M393_372Plasma
SA167396BL_200220_M393_373Plasma
SA167397BL_200220_M393_380Plasma
SA167398BL_200220_M393_381Plasma
SA167399BL_200220_M393_387Plasma
SA167400BL_200220_M393_388Plasma
SA167401BL_200220_M393_389Plasma
SA167402BL_200220_M393_390Plasma
SA167403BL_200220_M393_386Plasma
SA167404BL_200220_M393_385Plasma
SA167405BL_200220_M393_382Plasma
SA167406BL_200220_M393_383Plasma
SA167407BL_200220_M393_384Plasma
SA167408BL_200220_M393_369Plasma
SA167409BL_200220_M393_368Plasma
SA167410BL_200220_M393_353Plasma
SA167411BL_200220_M393_354Plasma
SA167412BL_200220_M393_355Plasma
SA167413BL_200220_M393_356Plasma
SA167414BL_200220_M393_352Plasma
SA167415BL_200220_M393_351Plasma
SA167416BL_200220_M393_347Plasma
SA167417BL_200220_M393_348Plasma
SA167418BL_200220_M393_280Plasma
SA167419BL_200220_M393_350Plasma
SA167420BL_200220_M393_357Plasma
SA167421BL_200220_M393_358Plasma
SA167422BL_200220_M393_364Plasma
SA167423BL_200220_M393_365Plasma
SA167424BL_200220_M393_366Plasma
SA167425BL_200220_M393_367Plasma
SA167426BL_200220_M393_363Plasma
SA167427BL_200220_M393_362Plasma
SA167428BL_200220_M393_359Plasma
SA167429BL_200220_M393_360Plasma
SA167430BL_200220_M393_361Plasma
SA167431BL_200220_M393_346Plasma
SA167432BL_200220_M393_282Plasma
SA167433BL_200220_M393_207Plasma
SA167434BL_200220_M393_206Plasma
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Collection:

Collection ID:CO001871
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:TR001891
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:SP001884
Sampleprep Summary:Same as treatment

Combined analysis:

Analysis ID AN002923
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

Chromatography:

Chromatography ID:CH002165
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:MS002715
Analysis ID:AN002923
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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