Summary of Study ST001803

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 ID	ST001803
Study Title	Human thyroid exposomics analysis
Study Type	Untargeted MS anlaysis
Study Summary	In the small number of thyroids that was analyzed with XLE, 14 environmental chemicals were quantified. The most prevalent was p,p’-DDE, detected in 4 out of 5 thyroid samples, with median concentration (2.20 ng/g). The amounts of individual chemicals were highly variable among the individuals, and the small number of samples precludes any generalization. Nevertheless, HCA of correlation matrix showed high correlation of chemicals measured in the thyroid samples was similar to that in the lung and plasma.
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
Email	xin.hu2@emory.edu
Phone	4047275091
Submit Date	2021-05-07
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	GC-MS
Release Date	2021-05-28
Release Version	1

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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:	SU001880
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
SA167569	ExStd5	external std
SA167570	Qstd_2_2	pooled plasma
SA167571	Qstd_2_1	pooled plasma
SA167572	Qstd_1_2	pooled plasma
SA167573	Qstd_1_1	pooled plasma
SA167565	NIST1957_1	SRM1957
SA167566	NIST1957_2	SRM1957
SA167567	NIST1958_1	SRM1958
SA167568	NIST1958_2	SRM1958
SA167574	T4_1	thyroid
SA167575	T4_2	thyroid
SA167576	T5_2	thyroid
SA167577	T3_2	thyroid
SA167578	T5_1	thyroid
SA167579	T1_1	thyroid
SA167580	T1_2	thyroid
SA167581	T3_1	thyroid
SA167582	T2_1	thyroid
SA167583	T2_2	thyroid
SA167584	IsoOctane.1	wash

Showing results 1 to 20 of 20

Showing results 1 to 20 of 20

Collection:

Collection ID:	CO001873
Collection Summary:	). Whole human thyroids from five individuals were post-mortem tissues that were acquired from National Disease Research Interchange (NDRI, Philadelphia, PA).
Sample Type:	Thyroid

Treatment:

Treatment ID:	TR001893
Treatment Summary:	Tissue materials were processed similarly with a consistent ratio of 1:5 (sample to hexane-ethyl acetate mixture), i.e., 100 mg lung was homogenized in 300 µL water and extracted with 150 µL formic acid and 400 µL hexane-ethyl acetate mixture, while 40 mg thyroid was homogenized in 250 µL water and extracted with 50 µL formic acid and 200 µL hexane-ethyl acetate mixture. Stool samples (100 mg) were homogenized and extracted directly in 50 µL formic acid and 500 µL hexane-ethyl acetate mixture and then processed as plasma samples. The variation of 1:4 from 1:5 in lung extraction was arbitrary in consideration of the lower density of lung as an organ. The internal standards were spiked at 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) for testing of QuEChERS based procedure, 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.

Treatment ID:

TR001893

Treatment Summary:

Tissue materials were processed similarly with a consistent ratio of 1:5 (sample to hexane-ethyl acetate mixture), i.e., 100 mg lung was homogenized in 300 µL water and extracted with 150 µL formic acid and 400 µL hexane-ethyl acetate mixture, while 40 mg thyroid was homogenized in 250 µL water and extracted with 50 µL formic acid and 200 µL hexane-ethyl acetate mixture. Stool samples (100 mg) were homogenized and extracted directly in 50 µL formic acid and 500 µL hexane-ethyl acetate mixture and then processed as plasma samples. The variation of 1:4 from 1:5 in lung extraction was arbitrary in consideration of the lower density of lung as an organ. The internal standards were spiked at 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) for testing of QuEChERS based procedure, 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.

Sample Preparation:

Sampleprep ID:	SP001886
Sampleprep Summary:	Same as treatment

Combined analysis:

Analysis ID	AN002925
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:	CH002167
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:	MS002716
Analysis ID:	AN002925
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