Summary of Study ST001804
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.
| Study ID | ST001804 |
| Study Title | Human stool exposomics analysis |
| Study Type | Untargeted MS anlaysis |
| Study Summary | Human stool samples, as a noninvasive matrix, have unique value in exposome research but have not been extensively studied for environmental chemical exposures. For lipophilic and unabsorbed dietary environmental chemicals, stool is a primary route of elimination and can therefore provide useful information on body burden and clearance of chemicals. In a pilot analysis of six human stool samples, we detected 52 and quantified 21 environmental chemicals, with HCB found in all samples. Quantification of HCB showed a median concentration of 0.057 ng/g. HCA of correlation matrix showed co-exposures of chemicals are likely as shown in the plasma, lung and thyroid. The high correlations of these persistent chemicals are not surprising as they likely derive from similar environmental exposure events. |
| 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 |
| 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 |
Select appropriate tab below to view additional metadata details:
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: | SU001881 |
| 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 |
|---|---|---|
| SA167593 | Exstd5_1219_1 | external std |
| SA167594 | Exstd5_1219_2 | external std |
| SA167595 | Exstd5_1219 | external std |
| SA167596 | Exstd5_1019_2 | external std |
| SA167597 | Exstd5_1019 | external std |
| SA167598 | Exstd5_1019_1 | external std |
| SA167585 | NIST1957_2 | SRM1957 |
| SA167586 | NIST1957_1 | SRM1957 |
| SA167587 | NIST1957_3 | SRM1957 |
| SA167588 | NIST1957_4 | SRM1957 |
| SA167589 | NIST1958_4 | SRM1958 |
| SA167590 | NIST1958_1 | SRM1958 |
| SA167591 | NIST1958_3 | SRM1958 |
| SA167592 | NIST1958_2 | SRM1958 |
| SA167599 | BL_12172019_006 | stool |
| SA167600 | BL_12172019_007 | stool |
| SA167601 | BL_12172019_005 | stool |
| SA167602 | BL_12172019_003 | stool |
| SA167603 | BL_12172019_002 | stool |
| SA167604 | BL_12172019_008 | stool |
| SA167605 | BL_12172019_004 | stool |
| SA167606 | BL_12172019_009 | stool |
| SA167607 | BL_12172019_012 | stool |
| SA167608 | BL_12172019_001 | stool |
| SA167609 | BL_12172019_010 | stool |
| SA167610 | BL_12172019_011 | stool |
| SA167611 | Isooctane_3 | wash |
| SA167612 | Isooctane_1 | wash |
| Showing results 1 to 28 of 28 |
Collection:
| Collection ID: | CO001874 |
| Collection Summary: | Human stool samples were obtained from PROGRESS, a biobank for cholestatic liver disease (IRB 670-02; Mayo Clinic, Rochester, MN), to test suitability of XLE for environmental chemical measurements in stool of patients with primary sclerosing cholangitis (PSC). |
| Sample Type: | Feces |
Treatment:
| Treatment ID: | TR001894 |
| 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: | SP001887 |
| Sampleprep Summary: | Same as treatment |
Combined analysis:
| Analysis ID | AN002926 |
|---|---|
| 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: | CH002168 |
| 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: | MS002717 |
| Analysis ID: | AN002926 |
| 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 |
