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.
| Study ID | ST001932 |
| Study Title | Perfluorinated compounds and high fat diet in relation to CVD-relevant metabolomic pathways in the SEARCH for Diabetes in Youth study |
| Study 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 | Clincal Biomarkers Laboratory |
| Last Name | Tran |
| First Name | ViLinh |
| Address | 615 Michael St, suite 225 |
| vtran6@emory.edu | |
| Phone | 4047275091 |
| Submit Date | 2021-10-06 |
| Total Subjects | 1796 |
| Study Comments | Both CHEAR pooled plasma samples and Clinical Biomarker Laboratory pooled plasma samples were used |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Chear Study | Yes |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-10-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA179607 | chearplasma_30f_1 | plasma |
| SA179608 | Q-Std Plasma pool_30b_1 | plasma |
| SA179609 | Q-Std Plasma pool_31a_1 | plasma |
| SA179610 | chearplasma_30e_1 | plasma |
| SA179611 | C-1MF95-S-00_1 | plasma |
| SA179612 | C-1M3X5-S-00_1 | plasma |
| SA179613 | C-1MF87-S-00_1 | plasma |
| SA179614 | chearplasma_31a_1 | plasma |
| SA179615 | chearplasma_31b_1 | plasma |
| SA179616 | C-1MQJ6-S-00_1 | plasma |
| SA179617 | C-1MQK4-S-00_1 | plasma |
| SA179618 | C-1MGE7-S-00_1 | plasma |
| SA179619 | C-1MGD9-S-00_1 | plasma |
| SA179620 | C-1M8K9-S-00_1 | plasma |
| SA179621 | C-1M8L7-S-00_1 | plasma |
| SA179622 | C-1M3W8-S-00_1 | plasma |
| SA179623 | C-1M7C8-S-00_1 | plasma |
| SA179624 | C-1LSU2-S-00_1 | plasma |
| SA179625 | C-1LSV0-S-00_1 | plasma |
| SA179626 | C-1LC41-S-00_1 | plasma |
| SA179627 | C-1LW82-S-00_1 | plasma |
| SA179628 | C-1LW74-S-00_1 | plasma |
| SA179629 | C-1LJD8-S-00_1 | plasma |
| SA179630 | C-1LJE6-S-00_1 | plasma |
| SA179631 | C-1LC58-S-00_1 | plasma |
| SA179632 | C-1M1U4-S-00_1 | plasma |
| SA179633 | C-1M9Q5-S-00_1 | plasma |
| SA179634 | C-1LLS3-S-00_1 | plasma |
| SA179635 | C-1M9P7-S-00_1 | plasma |
| SA179636 | C-1LRS7-S-00_1 | plasma |
| SA179637 | C-1M1V2-S-00_1 | plasma |
| SA179638 | C-1LRR0-S-00_1 | plasma |
| SA179639 | C-1M7D5-S-00_1 | plasma |
| SA179640 | C-1LYV4-S-00_1 | plasma |
| SA179641 | C-1MKC8-S-00_1 | plasma |
| SA179642 | C-1MV99-S-00_1 | plasma |
| SA179643 | C-1MVA1-S-00_1 | plasma |
| SA179644 | C-1MKB0-S-00_1 | plasma |
| SA179645 | C-1LT85-S-00_1 | plasma |
| SA179646 | C-1ME70-S-00_1 | plasma |
| SA179647 | C-1LT77-S-00_1 | plasma |
| SA179648 | C-1MUR5-S-00_1 | plasma |
| SA179649 | C-1MUS2-S-00_1 | plasma |
| SA179650 | C-1LDB9-S-00_1 | plasma |
| SA179651 | C-1LDC7-S-00_1 | plasma |
| SA179652 | C-1LZV3-S-00_1 | plasma |
| SA179653 | C-1LZU5-S-00_1 | plasma |
| SA179654 | C-1MN22-S-00_1 | plasma |
| SA179655 | C-1MN30-S-00_1 | plasma |
| SA179656 | C-1ME62-S-00_1 | plasma |
| SA179657 | C-1LX32-S-00_1 | plasma |
| SA179658 | C-1MQQ1-S-00_1 | plasma |
| SA179659 | C-1MQR9-S-00_1 | plasma |
| SA179660 | C-1LCL8-S-00_1 | plasma |
| SA179661 | C-1LSK4-S-00_1 | plasma |
| SA179662 | C-1LSJ6-S-00_1 | plasma |
| SA179663 | chearplasma_30d_1 | plasma |
| SA179664 | C-1LYW2-S-00_1 | plasma |
| SA179665 | C-1LCM6-S-00_1 | plasma |
| SA179666 | C-1LZS9-S-00_1 | plasma |
| SA179667 | chearplasma_31d_1 | plasma |
| SA179668 | C-1LX24-S-00_1 | plasma |
| SA179669 | chearplasma_31c_1 | plasma |
| SA179670 | C-1M7P9-S-00_1 | plasma |
| SA179671 | C-1LZT7-S-00_1 | plasma |
| SA179672 | C-1M7N3-S-00_1 | plasma |
| SA179673 | C-1LLT1-S-00_1 | plasma |
| SA179674 | chearplasma_30c_1 | plasma |
| SA179675 | C-1ME88-S-00_1 | plasma |
| SA179676 | C-1ME96-S-00_1 | plasma |
| SA179677 | C-1LZ63-S-00_1 | plasma |
| SA179678 | C-1LY49-S-00_1 | plasma |
| SA179679 | C-1LY31-S-00_1 | plasma |
| SA179680 | chearplasma_29c_1 | plasma |
| SA179681 | chearplasma_29d_1 | plasma |
| SA179682 | C-1LZ71-S-00_1 | plasma |
| SA179683 | C-1LSN7-S-00_1 | plasma |
| SA179684 | C-1LF71-S-00_1 | plasma |
| SA179685 | C-1LR53-S-00_1 | plasma |
| SA179686 | C-1LF63-S-00_1 | plasma |
| SA179687 | C-1M8J1-S-00_1 | plasma |
| SA179688 | C-1LSP3-S-00_1 | plasma |
| SA179689 | C-1M8H6-S-00_1 | plasma |
| SA179690 | C-1MPG4-S-00_1 | plasma |
| SA179691 | C-1MPF6-S-00_1 | plasma |
| SA179692 | C-1LZ14-S-00_1 | plasma |
| SA179693 | C-1MD97-S-00_1 | plasma |
| SA179694 | C-1MDA9-S-00_1 | plasma |
| SA179695 | C-1LZ06-S-00_1 | plasma |
| SA179696 | C-1MS68-S-00_1 | plasma |
| SA179697 | C-1M352-S-00_1 | plasma |
| SA179698 | C-1MS50-S-00_1 | plasma |
| SA179699 | C-1LP97-S-00_1 | plasma |
| SA179700 | C-1LPA9-S-00_1 | plasma |
| SA179701 | C-1MXR2-S-00_1 | plasma |
| SA179702 | C-1MXS9-S-00_1 | plasma |
| SA179703 | C-1LK84-S-00_1 | plasma |
| SA179704 | C-1LK76-S-00_1 | plasma |
| SA179705 | C-1LZ22-S-00_1 | plasma |
| SA179706 | C-1LZ30-S-00_1 | plasma |
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 |
