Summary of Study ST001932

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 PR001221. The data can be accessed directly via it's Project DOI: 10.21228/M8W682 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 IDST001932
Study TitlePerfluorinated compounds and high fat diet in relation to CVD-relevant metabolomic pathways in the SEARCH for Diabetes in Youth study
Study SummaryThis project aims to evaluate the association between environmental exposure to perfluorinated alkyl substances (PFCs) and the development of risk factors for cardiometabolic disease in youth diagnosed with diabetes in the SEARCH Cohort Study. The longitudinal study of newly diagnosed cases of type 1 and type 2 diabetes examines serum metabolome changes at baseline and follow-up at approximately 5 years (all >3 years from baseline). Exposures to PFCs and biological effects characterized by serum metabolome changes will be associated with known cardiometabolic risk factors in youth diagnosed with diabetes.
Institute
Emory University
DepartmentSchool of Medicine
LaboratoryClincal Biomarkers Laboratory
Last NameTran
First NameViLinh
Address615 Michael St, suite 225
Emailvtran6@emory.edu
Phone4047275091
Submit Date2021-10-06
Total Subjects1796
Study CommentsBoth CHEAR pooled plasma samples and Clinical Biomarker Laboratory pooled plasma samples were used
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2022-10-07
Release Version1
ViLinh Tran ViLinh Tran
https://dx.doi.org/10.21228/M8W682
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001221
Project DOI:doi: 10.21228/M8W682
Project Title:Perfluorinated compounds and high fat diet in relation to CVD-relevant metabolomic pathways in the SEARCH for Diabetes in Youth study
Project Type:NIH/NIEHS U2CES025660
Project Summary:This project aims to evaluate the association between environmental exposure to perfluorinated alkyl substances (PFCs) and the development of risk factors for cardiometabolic disease in youth diagnosed with diabetes in the SEARCH Cohort Study. The longitudinal study of newly diagnosed cases of type 1 and type 2 diabetes examines serum metabolome changes at baseline and follow-up at approximately 5 years (all >3 years from baseline). Exposures to PFCs and biological effects characterized by serum metabolome changes will be associated with known cardiometabolic risk factors in youth diagnosed with diabetes.
Institute:Emory University
Department:School of Medicine
Laboratory:Clinical Biomarkers Laboratory
Last Name:Tran
First Name:ViLinh
Address:615 Michael St, suite 225
Email:vtran6@emory.edu
Phone:4047275091
Funding Source:NIH/NIEHS U2CES025660

Subject:

Subject ID:SU002010
Subject Type:plasma
Subject Species:Homo sapiens
Age Or Age Range:children ages 20 and younger
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id FACTORS
SA179607chearplasma_30f_1plasma
SA179608Q-Std Plasma pool_30b_1plasma
SA179609Q-Std Plasma pool_31a_1plasma
SA179610chearplasma_30e_1plasma
SA179611C-1MF95-S-00_1plasma
SA179612C-1M3X5-S-00_1plasma
SA179613C-1MF87-S-00_1plasma
SA179614chearplasma_31a_1plasma
SA179615chearplasma_31b_1plasma
SA179616C-1MQJ6-S-00_1plasma
SA179617C-1MQK4-S-00_1plasma
SA179618C-1MGE7-S-00_1plasma
SA179619C-1MGD9-S-00_1plasma
SA179620C-1M8K9-S-00_1plasma
SA179621C-1M8L7-S-00_1plasma
SA179622C-1M3W8-S-00_1plasma
SA179623C-1M7C8-S-00_1plasma
SA179624C-1LSU2-S-00_1plasma
SA179625C-1LSV0-S-00_1plasma
SA179626C-1LC41-S-00_1plasma
SA179627C-1LW82-S-00_1plasma
SA179628C-1LW74-S-00_1plasma
SA179629C-1LJD8-S-00_1plasma
SA179630C-1LJE6-S-00_1plasma
SA179631C-1LC58-S-00_1plasma
SA179632C-1M1U4-S-00_1plasma
SA179633C-1M9Q5-S-00_1plasma
SA179634C-1LLS3-S-00_1plasma
SA179635C-1M9P7-S-00_1plasma
SA179636C-1LRS7-S-00_1plasma
SA179637C-1M1V2-S-00_1plasma
SA179638C-1LRR0-S-00_1plasma
SA179639C-1M7D5-S-00_1plasma
SA179640C-1LYV4-S-00_1plasma
SA179641C-1MKC8-S-00_1plasma
SA179642C-1MV99-S-00_1plasma
SA179643C-1MVA1-S-00_1plasma
SA179644C-1MKB0-S-00_1plasma
SA179645C-1LT85-S-00_1plasma
SA179646C-1ME70-S-00_1plasma
SA179647C-1LT77-S-00_1plasma
SA179648C-1MUR5-S-00_1plasma
SA179649C-1MUS2-S-00_1plasma
SA179650C-1LDB9-S-00_1plasma
SA179651C-1LDC7-S-00_1plasma
SA179652C-1LZV3-S-00_1plasma
SA179653C-1LZU5-S-00_1plasma
SA179654C-1MN22-S-00_1plasma
SA179655C-1MN30-S-00_1plasma
SA179656C-1ME62-S-00_1plasma
SA179657C-1LX32-S-00_1plasma
SA179658C-1MQQ1-S-00_1plasma
SA179659C-1MQR9-S-00_1plasma
SA179660C-1LCL8-S-00_1plasma
SA179661C-1LSK4-S-00_1plasma
SA179662C-1LSJ6-S-00_1plasma
SA179663chearplasma_30d_1plasma
SA179664C-1LYW2-S-00_1plasma
SA179665C-1LCM6-S-00_1plasma
SA179666C-1LZS9-S-00_1plasma
SA179667chearplasma_31d_1plasma
SA179668C-1LX24-S-00_1plasma
SA179669chearplasma_31c_1plasma
SA179670C-1M7P9-S-00_1plasma
SA179671C-1LZT7-S-00_1plasma
SA179672C-1M7N3-S-00_1plasma
SA179673C-1LLT1-S-00_1plasma
SA179674chearplasma_30c_1plasma
SA179675C-1ME88-S-00_1plasma
SA179676C-1ME96-S-00_1plasma
SA179677C-1LZ63-S-00_1plasma
SA179678C-1LY49-S-00_1plasma
SA179679C-1LY31-S-00_1plasma
SA179680chearplasma_29c_1plasma
SA179681chearplasma_29d_1plasma
SA179682C-1LZ71-S-00_1plasma
SA179683C-1LSN7-S-00_1plasma
SA179684C-1LF71-S-00_1plasma
SA179685C-1LR53-S-00_1plasma
SA179686C-1LF63-S-00_1plasma
SA179687C-1M8J1-S-00_1plasma
SA179688C-1LSP3-S-00_1plasma
SA179689C-1M8H6-S-00_1plasma
SA179690C-1MPG4-S-00_1plasma
SA179691C-1MPF6-S-00_1plasma
SA179692C-1LZ14-S-00_1plasma
SA179693C-1MD97-S-00_1plasma
SA179694C-1MDA9-S-00_1plasma
SA179695C-1LZ06-S-00_1plasma
SA179696C-1MS68-S-00_1plasma
SA179697C-1M352-S-00_1plasma
SA179698C-1MS50-S-00_1plasma
SA179699C-1LP97-S-00_1plasma
SA179700C-1LPA9-S-00_1plasma
SA179701C-1MXR2-S-00_1plasma
SA179702C-1MXS9-S-00_1plasma
SA179703C-1LK84-S-00_1plasma
SA179704C-1LK76-S-00_1plasma
SA179705C-1LZ22-S-00_1plasma
SA179706C-1LZ30-S-00_1plasma
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Collection:

Collection ID:CO002003
Collection Summary:Blood serum samples were collected from participants in the SEARCH multi-center, longitudinal cohort study at baseline and >3 years from baseline. Serum was obtained from blood vein draw in children (<20 years of age) with incidence or clinical presentation of type 1 and type 2 diabetes. Blood samples were collected in red top vacutainer tubes and sit upright for 30 minutes for clot formation, followed by centrifugation and removal of 500ul aliquots of serum to 1.8ml freezer tubes and stored in a -70C freezer. The samples were shipped on dry ice from the clinical centers to the CHEAR URR at Emory University.
Sample Type:plasma
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR002022
Treatment Summary:Samples were received frozen in aliquouts of <250uL. Freeze-thaw history for study samples prior to receipt by the EMORY URR is provided in the Study Design section. Prior to analysis, samples were thawed and prepared for HRM analysis using the standard protocols described in the Sample Preparation section.

Sample Preparation:

Sampleprep ID:SP002016
Sampleprep Summary:Samples were prepared for metabolomics analysis using established methods(Johnson et al. (2010). Analyst; Go et al. (2015). Tox Sci). Prior to analysis, plasma aliquots were removed from storage at -80 degrees C and thawed on ice. Each cryotube was then vortexed briefly to ensure homogeneity, and 50 microliters was transferred to a clean microfuge tube. Immediately after, the plasma was treated with 100 microliters of ice-cold LC-MS grade acetonitrile (Sigma Aldrich) containing 2.5 microliters of internal standard solution with eight stable isotopic chemicals selected to cover a range of chemical properties. Following addition of acetonitrile, urine was equilibrated for 30min on ice, upon which precipitated proteins were removed by centrifuge (14,000 rpm at 4 degrees C for 10 min). The resulting supernatant (100 microliters) was removed, added to a low volume autosampler vial and maintained at 4 degrees C until analysis (<22 h).
Sampleprep Protocol ID:HRM_SP_082016_01
Sampleprep Protocol Filename:EmoryUniversity_HRM_SP_082016_01.pdf
Sampleprep Protocol Comments:Date effective: 30 July 2016
Processing Storage Conditions:-80℃
Extraction Method:2:1 acetonitrile: sample followed by vortexing and centrifugation
Extract Storage:On ice

Combined analysis:

Analysis ID AN003141 AN003142
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Dionex UltiMate 3000 Dionex UltiMate 3000
Column Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002323
Chromatography Summary:The HILIC column is operated parallel to reverse phase column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6-port switching valves. During operation of HILIC separation method, the MS is operated in positive ion mode and 10 microliters of sample is injected onto the HILIC column while the reverse phase column is flushing with wash solution. Flow rate is maintained at 0.35 mL/min until 1.5 min, increased to 0.4 mL/min at 4 min and held for 1 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 2% formic acid (v/v) in LC-MS grade water. Initial mobile phase conditions are 22.5% A, 75% B, 2.5% C hold for 1.5 min, with linear gradient to 77.5% A, 20% B, 2.5% C at 4 min, hold for 1 min, resulting in a total analytical run time of 5 min. During the flushing phase (reverse phase analytical separation), the HILIC column is equilibrated with a wash solution of 77.5% A, 20% B, 2.5% C.
Methods ID:2% formic acid in LC-MS grade water
Methods Filename:20160920_posHILIC120kres5min_ESI_c18negwash.meth
Chromatography Comments:Triplicate injections for each chromatography mode
Instrument Name:Dionex UltiMate 3000
Column Name:Waters XBridge BEH Amide XP HILIC (50 x 2.1mm x 2.5um) with Thermo Accucore HILIC guard
Column Temperature:60C
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:HILIC
  
Chromatography ID:CH002324
Chromatography Summary:The C18 column is operated parallel to the HILIC column for simultaneous analytical separation and column flushing through the use of a dual head HPLC pump equipped with 10-port and 6- port switching valves. During operation of the C18 method, the MS is operated in negative ion mode and 10 μL of sample is injected onto the C18 column while the HILIC column is flushing with wash solution. Flow rate is maintained at 0.4 mL/min until 1.5 min, increased to 0.5 mL/min at 2 min and held for 3 min. Solvent A is 100% LC-MS grade water, solvent B is 100% LC-MS grade acetonitrile and solvent C is 10mM ammonium acetate in LC-MS grade water. Initial mobile phase conditions are 60% A, 35% B, 5% C hold for 0.5 min, with linear gradient to 0% A, 95% B, 5% C at 1.5 min, hold for 3.5 min, resulting in a total analytical run time of 5 min. During the flushing phase (HILIC analytical separation), the C18 column is equilibrated with a wash solution of 0% A, 95% B, 5% C until 2.5 min, followed by an equilibration solution of 60% A, 35% B, 5% C for 2.5 min.
Methods ID:10mM ammonium acetate in LC-MS grade water
Methods Filename:20160920_negC18120kres5min_ESI_HILICposwash.meth
Instrument Name:Dionex UltiMate 3000
Column Name:Higgins endcapped C18 stainless steel (50 x 2.1mm,3um),Product #TS-0521-C183; Thermo Accucore C18 guard with holder,Product #17126-014005
Column Temperature:60C
Flow Rate:0.4 mL/min for 1.5 min; linear increase to 0.5 mL/min at 2 min held for 3 min
Sample Injection:10 uL
Solvent A:100% water
Solvent B:100% acetonitrile
Analytical Time:5 min
Sample Loop Size:15 uL
Sample Syringe Size:100 uL
Chromatography Type:Reversed phase

MS:

MS ID:MS002921
Analysis ID:AN003141
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:no comments
Ion Mode:POSITIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:3500
Activation Parameter:5.00E+05
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
  
MS ID:MS002922
Analysis ID:AN003142
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:no comments
Ion Mode:NEGATIVE
Capillary Temperature:250C
Collision Gas:N2
Dry Gas Flow:45
Dry Gas Temp:150C
Mass Accuracy:< 3ppm
Spray Voltage:-4000
Activation Parameter:5.00E+05
Activation Time:118ms
Interface Voltage:S-Lens RF level= 55
Analysis Protocol File:EmoryUniversity_HRM_QEHF-MS_092017_v1.pdf
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