Summary of Study ST002436

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 PR001568. The data can be accessed directly via it's Project DOI: 10.21228/M8142B 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 IDST002436
Study TitleDiscovery of phytochelatins in human urine: Evidence for function in selenium disposition and protection against cadmium
Study SummaryThe goal of this project was to detect phytochelatins, plant-derived peptides which function as metal chelators, in human urine. Untargeted metabolomics of 143 urine samples from healthy adults was performed. Phytochelatin 2, γE-C-γE-C-G, was detected, and the rest of the urine metabolome was searched for phytochelatins and predicted phytochelatin metabolites which correlated with phytochelatin 2 concentrations. Phytochelatin 2 and associated metabolites were found to correlate with urinary metals, and further experiments were performed provide insight into function of dietary phytochelatins.
Institute
Emory University
Last NameJarrell
First NameZachery
Address615 Michael St
Emailzjarrel@emory.edu
Phone4047275984
Submit Date2023-01-10
Total Subjects143
Num Males37
Num Females106
Analysis Type DetailLC-MS
Release Date2023-01-25
Release Version1
Zachery Jarrell Zachery Jarrell
https://dx.doi.org/10.21228/M8142B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001568
Project DOI:doi: 10.21228/M8142B
Project Title:Detection phytochelatins in human urine
Project Type:Untargeted LC-MS metabolomics analysis
Project Summary:The goal of this project was to detect phytochelatins, plant-derived peptides which function as metal chelators, in human urine. Untargeted metabolomics of 143 urine samples from healthy adults was performed. Phytochelatin 2, γE-C-γE-C-G, was detected, and the rest of the urine metabolome was searched for phytochelatins and predicted phytochelatin metabolites which correlated with phytochelatin 2 concentrations. Phytochelatin 2 and associated metabolites were found to correlate with urinary metals, and further experiments were performed provide insight into function of dietary phytochelatins.
Institute:Emory University
Department:Medicine, Pulmonary
Laboratory:Dean Jones
Last Name:Jarrell
First Name:Zachery
Address:615 Michael St
Email:zjarrel@emory.edu
Phone:4047275984
Funding Source:This work was supported by the Emory University Predictive Health Institute, the Woodruff Foundation (Atlanta, GA), National Institutes of Health Grant UL1 TR002378, and National Institute of Environmental Health Sciences Grants R01 ES031980 (YMG), R21 ES031824 (DPJ and YMG), and F32 ES033908 (ZRJ).
Contributors:Zachery R. Jarrell, Ken H. Liu, Kristine K. Dennis, Xin Hu, Greg S. Martin, Dean P. Jones, and Young-Mi Go

Subject:

Subject ID:SU002525
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:40-69
Weight Or Weight Range:100-350 lbs
Height Or Height Range:58-78 inches
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id S-S PyC2-Gly (uM)
SA243434chdwb-urine0360.661122479
SA243435chdwb-urine1000.896263219
SA243515chdwb-urine12210.26343373
SA243436chdwb-urine1121.073769761
SA243516chdwb-urine10210.90650247
SA243517chdwb-urine07811.33459235
SA243518chdwb-urine13511.4693434
SA243519chdwb-urine05811.89971283
SA243520chdwb-urine03211.91846821
SA243521chdwb-urine08712.10417182
SA243522chdwb-urine13312.20385185
SA243523chdwb-urine08912.21886353
SA243524chdwb-urine13412.54000382
SA243437chdwb-urine1081.305671401
SA243525chdwb-urine03813.48218633
SA243438chdwb-urine0731.355308771
SA243526chdwb-urine05213.84936927
SA243527chdwb-urine12914.33894598
SA243528chdwb-urine08814.35487877
SA243529chdwb-urine05414.58118808
SA243530chdwb-urine00214.74088918
SA243531chdwb-urine11615.31049025
SA243532chdwb-urine05115.6512718
SA243533chdwb-urine08215.78374491
SA243534chdwb-urine08615.7907918
SA243439chdwb-urine0261.649906706
SA243535chdwb-urine09616.70920489
SA243536chdwb-urine10916.80832584
SA243537chdwb-urine13617.39141836
SA243538chdwb-urine08417.42605527
SA243539chdwb-urine09417.51110809
SA243440chdwb-urine1421.777493937
SA243540chdwb-urine09018.40527598
SA243541chdwb-urine08019.13551849
SA243542chdwb-urine07019.32974437
SA243441chdwb-urine0171.962773038
SA243543chdwb-urine14019.74812495
SA243544chdwb-urine03020.16881392
SA243545chdwb-urine06721.24909392
SA243546chdwb-urine05521.3933348
SA243442chdwb-urine0272.144816242
SA243443chdwb-urine0332.191310627
SA243547chdwb-urine05322.14331628
SA243444chdwb-urine0152.389070356
SA243548chdwb-urine00124.14083515
SA243549chdwb-urine02124.17067909
SA243550chdwb-urine07624.33782275
SA243551chdwb-urine07224.6165696
SA243552chdwb-urine09525.26453704
SA243445chdwb-urine0202.60009726
SA243446chdwb-urine0072.611884254
SA243447chdwb-urine0432.636236777
SA243448chdwb-urine0062.647693773
SA243449chdwb-urine0602.70618981
SA243553chdwb-urine04427.12207937
SA243554chdwb-urine12827.29288984
SA243450chdwb-urine0082.729404964
SA243555chdwb-urine01927.31494841
SA243556chdwb-urine14127.43510269
SA243451chdwb-urine0492.946623324
SA243557chdwb-urine02929.92081902
SA243558chdwb-urine09830.2902847
SA243452chdwb-urine0413.033298892
SA243453chdwb-urine0043.194246294
SA243454chdwb-urine0373.205139411
SA243455chdwb-urine1063.208070941
SA243559chdwb-urine01332.90436841
SA243456chdwb-urine0313.44802708
SA243457chdwb-urine0453.451032299
SA243458chdwb-urine0503.540195663
SA243459chdwb-urine1203.592873494
SA243460chdwb-urine0233.642578145
SA243560chdwb-urine10136.45067543
SA243561chdwb-urine11536.55701788
SA243461chdwb-urine0143.697232757
SA243462chdwb-urine0713.916190811
SA243463chdwb-urine0923.927087132
SA243464chdwb-urine0913.981741743
SA243465chdwb-urine1214.007673769
SA243466chdwb-urine0254.01273266
SA243467chdwb-urine0284.081939194
SA243468chdwb-urine1304.369389322
SA243469chdwb-urine0934.371558334
SA243470chdwb-urine0114.424345096
SA243471chdwb-urine1234.605946167
SA243562chdwb-urine08146.94037201
SA243472chdwb-urine0664.697070293
SA243473chdwb-urine0104.773184344
SA243474chdwb-urine0654.793871655
SA243475chdwb-urine1044.907544532
SA243476chdwb-urine0035.10490538
SA243477chdwb-urine1195.122597083
SA243478chdwb-urine1325.302115647
SA243479chdwb-urine0695.424845831
SA243480chdwb-urine1395.635031722
SA243481chdwb-urine0565.677655847
SA243482chdwb-urine1115.682980659
SA243483chdwb-urine0405.699413246
SA243484chdwb-urine0575.722115783
SA243485chdwb-urine0245.849318552
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Collection:

Collection ID:CO002518
Collection Summary:Samples were collected using standard operating procedures in the Center for Health Discovery and Well Being (CHDWB) cohort of healthy adults. The CHDWB enrolled 763 participants starting in 2008 with approval from the Emory Institutional Review Board (IRB approval No. 00007243). The original study included both genders and included individuals self-identifying as white, black, Hispanic and Asian. The present study selected available archival samples from 143 individuals without known disease. Urine samples included one sample per individual that was collected at either baseline, 6 months, or 12 months. Urine samples were stored at -80 ºC prior to analysis
Sample Type:Urine

Treatment:

Treatment ID:TR002537
Treatment Summary:This study used archival samples from an observational study. No treatment was performed.

Sample Preparation:

Sampleprep ID:SP002531
Sampleprep Summary:Samples were prepared following the Emory University Clinical Biomarkers Laboratory SOP for high resolution metabolomics sample preparation. Urine was thawed from -80 °C on ice and vortexed to homogenize. 50 μL urine was transferred to a clean microcentrifuge tube and treated with with 100 μL LC-MS grade acetonitrile containing 2.5 μL internal standard solution. Urine was equilibrated on ice for 30 min. Precipitated proteins were removed by centrifuge (16100 x g at 4 °C for 10 min). 100 μL supernatant was removed and added to an autosampler vial. Samples were maintained at 4 °C until analysis. Samples were prepared alongside NIST SRM 1950 and q3June2014 reference standards.
Sampleprep Protocol Filename:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf

Combined analysis:

Analysis ID AN003969
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000
Column Waters XBridge BEH Amide (50 x 2.1mm,2.5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH002935
Methods Filename:EmoryUniversity_HRM-QEHF_chromatography_5min_092017_v1.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters XBridge BEH Amide (50 x 2.1mm,2.5um)
Column Temperature:60
Flow Gradient:A= water, B= acetontrile, C= 2% formic acid in water; 22.5% A, 75% B, 2.5% C hold for 1.5 min, linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min
Flow Rate:0.35 mL/min for 1.5 min; linear increase to 0.4 mL/min at 4 min, hold for 1 min
Solvent A:100% water
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS003703
Analysis ID:AN003969
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw analysis files from urine analyses were converted to .mzXML using ProteoWizard v3. Data extraction was performed using apLCMS v6.3.3 and xMSanalyzer v2.0.8, generating m/z features consisting of an m/z, retention time (RT) and ion intensity. Feature and sample filtering retained features with a median CV of 50% or less, with a minimum mean Pearson correlation coefficient of 0.7 between technical replicates, and which were detected in at least 30% of samples. Technical replicates were median summarized.
Ion Mode:POSITIVE
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MassSpec_092017_v1.pdf
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