Summary of Study ST003415

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 PR001661. The data can be accessed directly via it's Project DOI: 10.21228/M80Q6D This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST003415
Study TitleRole of environmental toxicants in obesity-related cardiovascular disease- Part 3 GC-MS analysis of adipose tissue
Study SummaryLipophilic pollutants, particularly persistent organic pollutants (POPs), bioaccumulate in adipose tissue. We hypothesize that pollutants that accumulate in fat depots promote adipose tissue dysfunction, in part, by activating inflammatory and pro-atherogenic signaling pathways implicated in the pathogenesis of cardiovascular disease. Untargeted analyses of pollutants in adipose tissues and blood from lean individuals and obese subjects at the time of bariatric surgery, with repeat measures.
Institute
Boston University
Last NameNoyan
First NameGocke
AddressBoston University Medical Center
EmailNoyan.Gokce@bmc.org
Phone617414 1565
Submit Date2024-07-31
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailGC-MS
Release Date2025-08-22
Release Version1
Gocke Noyan Gocke Noyan
https://dx.doi.org/10.21228/M80Q6D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001661
Project DOI:doi: 10.21228/M80Q6D
Project Title:Untargeted analysis of plasma
Project Summary:Untargeted analysis of plasma from lean individuals and obese subjects at the time of bariatric surgery, with some repeat measures.
Institute:Icahn School of Medicine at Mount Sinai
Last Name:Petrick
First Name:Lauren
Address:1428 Madison Avenue, Atran Building
Email:lauren.petrick@mssm.edu
Phone:9739976141
Funding Source:Support was provided by the Human Health Exposure Analysis Resource Coordinating Center: Westat, Inc.: O’Brien B (U24 ES026539), and the Human Health Exposure Analysis Data Center: Icahn School of Medicine at Mount Sinai: Teitelbaum S (U2CES026555)

Subject:

Subject ID:SU003542
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 Sample source Timepoint_uom
SA376652B4_042_LQCAdipose tissue -
SA376653B11_015_LQCAdipose tissue -
SA376654B4_015_LQCAdipose tissue -
SA376655B4_016_LQCAdipose tissue -
SA376656B4_017_LQCAdipose tissue -
SA376657B4_028_LQCAdipose tissue -
SA376658B8_040_LQCAdipose tissue -
SA376659B10_050_LQCAdipose tissue -
SA376660B11_017_LQCAdipose tissue -
SA376661B10_049_LQCAdipose tissue -
SA376662B10_048_LQCAdipose tissue -
SA376663B4_048_LQCAdipose tissue -
SA376664B4_049_LQCAdipose tissue -
SA376665B4_050_LQCAdipose tissue -
SA376666B10_042_LQCAdipose tissue -
SA376667B10_040_LQCAdipose tissue -
SA376668B11_016_LQCAdipose tissue -
SA376669B3_050_LQCAdipose tissue -
SA376670B5_016_LQCAdipose tissue -
SA376671B11_040_LQCAdipose tissue -
SA376672B11_048_LQCAdipose tissue -
SA376673B9_017_LQCAdipose tissue -
SA376674B8_042_LQCAdipose tissue -
SA376675B11_042_LQCAdipose tissue -
SA376676B2_048_LQCAdipose tissue -
SA376677B2_049_LQCAdipose tissue -
SA376678B2_050_LQCAdipose tissue -
SA376679B3_015_LQCAdipose tissue -
SA376680B3_049_LQCAdipose tissue -
SA376681B3_016_LQCAdipose tissue -
SA376682B3_017_LQCAdipose tissue -
SA376683B3_028_LQCAdipose tissue -
SA376684B3_040_LQCAdipose tissue -
SA376685B3_042_LQCAdipose tissue -
SA376686B11_028_LQCAdipose tissue -
SA376687B3_048_LQCAdipose tissue -
SA376688B5_015_LQCAdipose tissue -
SA376689B5_017_LQCAdipose tissue -
SA376690B11_049_LQCAdipose tissue -
SA376691B7_040_LQCAdipose tissue -
SA376692B9_048_LQCAdipose tissue -
SA376693B9_042_LQCAdipose tissue -
SA376694B9_040_LQCAdipose tissue -
SA376695B7_015_LQCAdipose tissue -
SA376696B7_016_LQCAdipose tissue -
SA376697B7_017_LQCAdipose tissue -
SA376698B7_028_LQCAdipose tissue -
SA376699B7_042_LQCAdipose tissue -
SA376700B6_050_LQCAdipose tissue -
SA376701B7_048_LQCAdipose tissue -
SA376702B7_049_LQCAdipose tissue -
SA376703B7_050_LQCAdipose tissue -
SA376704B9_028_LQCAdipose tissue -
SA376705B8_015_LQCAdipose tissue -
SA376706B8_016_LQCAdipose tissue -
SA376707B8_017_LQCAdipose tissue -
SA376708B9_049_LQCAdipose tissue -
SA376709B6_049_LQCAdipose tissue -
SA376710B5_028_LQCAdipose tissue -
SA376711B6_016_LQCAdipose tissue -
SA376712B5_040_LQCAdipose tissue -
SA376713B5_042_LQCAdipose tissue -
SA376714B10_028_LQCAdipose tissue -
SA376715B5_048_LQCAdipose tissue -
SA376716B5_049_LQCAdipose tissue -
SA376717B5_050_LQCAdipose tissue -
SA376718B6_015_LQCAdipose tissue -
SA376719B6_017_LQCAdipose tissue -
SA376720B6_048_LQCAdipose tissue -
SA376721B6_028_LQCAdipose tissue -
SA376722B10_017_LQCAdipose tissue -
SA376723B6_040_LQCAdipose tissue -
SA376724B10_016_LQCAdipose tissue -
SA376725B6_042_LQCAdipose tissue -
SA376726B10_015_LQCAdipose tissue -
SA376727B9_050_LQCAdipose tissue -
SA376728B2_042_LQCAdipose tissue -
SA376729B4_040_LQCAdipose tissue -
SA376730B2_040_LQCAdipose tissue -
SA376731B1_040_LQCAdipose tissue -
SA376732B2_015_LQCAdipose tissue -
SA376733B9_016_LQCAdipose tissue -
SA376734B9_015_LQCAdipose tissue -
SA376735B12_015_LQCAdipose tissue -
SA376736B12_016_LQCAdipose tissue -
SA376737B12_017_LQCAdipose tissue -
SA376738B1_050_LQCAdipose tissue -
SA376739B1_049_LQCAdipose tissue -
SA376740B1_048_LQCAdipose tissue -
SA376741B1_042_LQCAdipose tissue -
SA376742B1_028_LQCAdipose tissue -
SA376743B2_017_LQCAdipose tissue -
SA376744B1_017_LQCAdipose tissue -
SA376745B1_016_LQCAdipose tissue -
SA376746B1_015_LQCAdipose tissue -
SA376747B12_028_LQCAdipose tissue -
SA376748B8_048_LQCAdipose tissue -
SA376749B8_049_LQCAdipose tissue -
SA376750B8_050_LQCAdipose tissue -
SA376751B12_048_LQCAdipose tissue -
Showing page 1 of 6     Results:    1  2  3  4  5  Next  Last     Showing results 1 to 100 of 528

Collection:

Collection ID:CO003535
Collection Summary:Adipose tissues were collected from different fat depots during two surgeries (biopsied before (Visit 1) and after (Visit 2) weight loss). Two types of body fat were collected: Subcutaneous and Visceral.
Sample Type:Adipose tissue

Treatment:

Treatment ID:TR003551
Treatment Summary:Measures before (visit_1) and after (visit_2) bariatric surgery.

Sample Preparation:

Sampleprep ID:SP003549
Sampleprep Summary:In the allocated randomized order, about 20 mg of frozen adipose tissue samples were weighed and transferred to lysing tubes. To the tubes, 100% LC-MS grade formic acid and extraction solvent (80% acetonitrile:ethyl acetate spiked with 10ppb of Internal Standards [IS]) were added and allowed to sit on ice for a minute. Following this, the tissues were mechanically homogenized at 4C. The tubes were then centrifuged at 12500 RPM for 5 min at 4°C and the supernatant was transferred to 1.5mL microcentrifuge tube containing 100μL water. The original lysing tubes was re-extracted again as above and the supernatant pooled, giving a final ratio of 4:1 (organic:aqueous). Phospholipids were removed using ISOLUTE PLD+ tubes as per the manufacture’s protocol. The eluent was collected in a 4 mL glass tubes containing 100μL of ice cold MQ water (7:1, organic:aqueous). 100% hexane was added to the glass tubes, vortexed for 60 mins, then stored at -20°C overnight. The tubes were then vortexed, centrifuged at 3500 rpm for 10min at 4°C, and the hexane fraction was transferred to a new tube containing pre-weighed dSPE powder to remove residual water and contaminants. The tubes were vortexed, centrifuged at3500 rpm for 10min at 4°C, and the supernatant transferred to 2mL GC vials and evaporated under a gentle stream of nitrogen to dryness. Vials were reconstituted with 300μL of 80% hexane:ethyl acetate for analysis. A small aliquot (10μL) from each sample across all batches was pooled together to prepare the pooled QC (LQC). The procedure blanks and external QC samples underwent the same extraction procedure using 100 μL of MilliQ water instead of tissue.

Combined analysis:

Analysis ID AN005614
Chromatography ID CH004265
MS ID MS005339
Analysis type MS
Chromatography type GC
Chromatography system Thermo Trace 1310
Column Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type EI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode POSITIVE
Units AU

Chromatography:

Chromatography ID:CH004265
Chromatography Summary:GC-MS
Instrument Name:Thermo Trace 1310
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Column Temperature:The oven temperature gradient was set at an initial temperature of 50°C held for 2.5 min, followed by ramp of 25°C/min to 180°C and held for 1 min and then to 250°C at a rate of 6°C/min and then raised to 320°C at a rate of 10°C/min and held for 15min
Flow Gradient:none
Flow Rate:none
Solvent A:none
Solvent B:none
Chromatography Type:GC

MS:

MS ID:MS005339
Analysis ID:AN005614
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:EI
MS Comments:The Programmable Temperature Variable (PTV) inlet was maintained at an initial temperature of 60°C with a split flow of 20mL/min. During the injection phases the PTV inlet was raised to 300°C in 1 min at a rate of 2.5°C/sec. The He carrier gas flow was maintained at a constant flow of 1.5mL/min operated under vacuum compensation mode. The transfer line temperature was maintained at 280°C throughout the run. On the MS, the analytes were scanned across a scan range of 65-975 m/z at 60000 resolution (FWHM) with an automated gain control set to 1e6. Both the MS transfer line and ion source temperatures were set at 280°C.
Ion Mode:POSITIVE
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