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.
Study ID | ST001801 |
Study Title | CHDWB human plasma exposomics analysis - 1 |
Study Type | Untargeted MS anlaysis |
Study Summary | We 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 |
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 | 2021-05-06 |
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: | SU001878 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | type |
---|---|---|
SA167335 | ExStd5_1 | External std |
SA167336 | ExStd5_3 | External std |
SA167337 | ExStd5_2 | External std |
SA167338 | ExStd5_4 | External std |
SA167339 | ExStd5_5 | External std |
SA167340 | BL_200220_M393_311 | Plasma |
SA167341 | BL_200220_M393_312 | Plasma |
SA167342 | BL_200220_M393_332 | Plasma |
SA167343 | BL_200220_M393_310 | Plasma |
SA167344 | BL_200220_M393_331 | Plasma |
SA167345 | BL_200220_M393_306 | Plasma |
SA167346 | BL_200220_M393_305 | Plasma |
SA167347 | BL_200220_M393_333 | Plasma |
SA167348 | BL_200220_M393_307 | Plasma |
SA167349 | BL_200220_M393_308 | Plasma |
SA167350 | BL_200220_M393_309 | Plasma |
SA167351 | BL_200220_M393_337 | Plasma |
SA167352 | BL_200220_M393_341 | Plasma |
SA167353 | BL_200220_M393_342 | Plasma |
SA167354 | BL_200220_M393_343 | Plasma |
SA167355 | BL_200220_M393_344 | Plasma |
SA167356 | BL_200220_M393_340 | Plasma |
SA167357 | BL_200220_M393_339 | Plasma |
SA167358 | BL_200220_M393_335 | Plasma |
SA167359 | BL_200220_M393_336 | Plasma |
SA167360 | BL_200220_M393_304 | Plasma |
SA167361 | BL_200220_M393_338 | Plasma |
SA167362 | BL_200220_M393_334 | Plasma |
SA167363 | BL_200220_M393_300 | Plasma |
SA167364 | BL_200220_M393_288 | Plasma |
SA167365 | BL_200220_M393_289 | Plasma |
SA167366 | BL_200220_M393_290 | Plasma |
SA167367 | BL_200220_M393_291 | Plasma |
SA167368 | BL_200220_M393_287 | Plasma |
SA167369 | BL_200220_M393_286 | Plasma |
SA167370 | BL_200220_M393_281 | Plasma |
SA167371 | BL_200220_M393_283 | Plasma |
SA167372 | BL_200220_M393_284 | Plasma |
SA167373 | BL_200220_M393_285 | Plasma |
SA167374 | BL_200220_M393_292 | Plasma |
SA167375 | BL_200220_M393_293 | Plasma |
SA167376 | BL_200220_M393_299 | Plasma |
SA167377 | BL_200220_M393_345 | Plasma |
SA167378 | BL_200220_M393_301 | Plasma |
SA167379 | BL_200220_M393_302 | Plasma |
SA167380 | BL_200220_M393_298 | Plasma |
SA167381 | BL_200220_M393_297 | Plasma |
SA167382 | BL_200220_M393_294 | Plasma |
SA167383 | BL_200220_M393_295 | Plasma |
SA167384 | BL_200220_M393_296 | Plasma |
SA167385 | BL_200220_M393_303 | Plasma |
SA167386 | BL_200220_M393_349 | Plasma |
SA167387 | BL_200220_M393_376 | Plasma |
SA167388 | BL_200220_M393_377 | Plasma |
SA167389 | BL_200220_M393_378 | Plasma |
SA167390 | BL_200220_M393_379 | Plasma |
SA167391 | BL_200220_M393_375 | Plasma |
SA167392 | BL_200220_M393_374 | Plasma |
SA167393 | BL_200220_M393_370 | Plasma |
SA167394 | BL_200220_M393_371 | Plasma |
SA167395 | BL_200220_M393_372 | Plasma |
SA167396 | BL_200220_M393_373 | Plasma |
SA167397 | BL_200220_M393_380 | Plasma |
SA167398 | BL_200220_M393_381 | Plasma |
SA167399 | BL_200220_M393_387 | Plasma |
SA167400 | BL_200220_M393_388 | Plasma |
SA167401 | BL_200220_M393_389 | Plasma |
SA167402 | BL_200220_M393_390 | Plasma |
SA167403 | BL_200220_M393_386 | Plasma |
SA167404 | BL_200220_M393_385 | Plasma |
SA167405 | BL_200220_M393_382 | Plasma |
SA167406 | BL_200220_M393_383 | Plasma |
SA167407 | BL_200220_M393_384 | Plasma |
SA167408 | BL_200220_M393_369 | Plasma |
SA167409 | BL_200220_M393_368 | Plasma |
SA167410 | BL_200220_M393_353 | Plasma |
SA167411 | BL_200220_M393_354 | Plasma |
SA167412 | BL_200220_M393_355 | Plasma |
SA167413 | BL_200220_M393_356 | Plasma |
SA167414 | BL_200220_M393_352 | Plasma |
SA167415 | BL_200220_M393_351 | Plasma |
SA167416 | BL_200220_M393_347 | Plasma |
SA167417 | BL_200220_M393_348 | Plasma |
SA167418 | BL_200220_M393_280 | Plasma |
SA167419 | BL_200220_M393_350 | Plasma |
SA167420 | BL_200220_M393_357 | Plasma |
SA167421 | BL_200220_M393_358 | Plasma |
SA167422 | BL_200220_M393_364 | Plasma |
SA167423 | BL_200220_M393_365 | Plasma |
SA167424 | BL_200220_M393_366 | Plasma |
SA167425 | BL_200220_M393_367 | Plasma |
SA167426 | BL_200220_M393_363 | Plasma |
SA167427 | BL_200220_M393_362 | Plasma |
SA167428 | BL_200220_M393_359 | Plasma |
SA167429 | BL_200220_M393_360 | Plasma |
SA167430 | BL_200220_M393_361 | Plasma |
SA167431 | BL_200220_M393_346 | Plasma |
SA167432 | BL_200220_M393_282 | Plasma |
SA167433 | BL_200220_M393_207 | Plasma |
SA167434 | BL_200220_M393_206 | Plasma |
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 |