Summary of Study ST001636

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 PR000950. The data can be accessed directly via it's Project DOI: 10.21228/M8WM4P 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 IDST001636
Study TitleTEDDY Lipidomics Study
Study SummaryLipids were quantified in human plasma from the 1:3 matched TEDDY case-control subjects (Lee et al., 2013). Blood plasma was extracted following the methyl-tert-butyl ether (MTBE) extraction protocols. The choice of internal standards and chromatographic conditions was optimized by using toluene in the reconstitution solvent mixture to ensure that very lipophilic components like cholesteryl esters (CEs) and triacylglycerols (TAGs) are efficiently transferred to the ultrahigh-pressure liquid chromatography (UHPLC) column in the injection process. Lipids were analyzed by charged surface hybrid column electrospray ionization quadrupole time of flight tandem mass spectrometer (CSH-ESI QTOF MS/MS). The analytical ultra-high-pressure liquid chromatography (UHPLC) column is protected by a short guard column which was replaced after 400 injections while the UHPLC column was replaced after 1,200 serum (or plasma) extract injections. The sequence of column replacements were evaluated to ensure no detrimental effects were detected with respect to peak shapes, absolute or relative lipid retention times or reproducibility of quantifications. Automatic valve switching was used after each injection to reduce sample carryover for highly lipophilic compounds. This valve switching employed a dual solvent wash, first with a water/acetonitrile mixture (1:1, v/v) and subsequently with a 100% isopropanol wash. LC-BinBase was used as an untargeted approach for annotating chromatographic peaks and spectra against a dynamically built library of compounds. The quantified raw dataset was normalized by the SERRF bioinformatics pipeline [1]. In the LC-QTOF data, samples were removed before normalization if they failed the laboratory’s QC standards or were missing data for more than half of the compounds. The SERRF normalized data have been made available for identified compounds. Results data for unidentified compounds are available un-normalized. An explanation of the study design variables are explained in detail in a data dictionary provided in the raw data download section. References: 1) Lee HS, Burkhardt B, McLeod W, Smith S, Eberhard C, Lynch K, Hadley D, Rewers M, Simell O, She JX, Hagopian W, Lernmark A, Akolkar B, Ziegler AG, Krischer J, and the TEDDY Study Group: Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Diabetes/Metabolism Research and Reviews. Epub 2013 December 15. doi: 10.1002/dmrr.2510 (PubMed ID: 24339168). 2) Fan S, Kind T, Cajka T, Hazen SL, Tang WHW, Kaddurah-Daouk R, Irvin MR, Arnett DK, Barupal DK, Fiehn O: Systematic Error Removal Using Random Forest for Normalizing Large-Scale Untargeted Lipidomics Data. Anal Chem 2019, 91(5):3590-3596.
Institute
University of South Florida
Last NameKrischer
First NameJeffrey
Address3650 Spectrum Blvd
EmailTEDDYDataPlatform@epi.usf.edu
Phone813-396-9512
Submit Date2020-12-21
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-01-25
Release Version1
Jeffrey Krischer Jeffrey Krischer
https://dx.doi.org/10.21228/M8WM4P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000950
Project DOI:doi: 10.21228/M8WM4P
Project Title:TEDDY Metabolomics Study
Project Summary:The quantification of primary metabolites in human plasma from TEDDY case-control subjects. The TEDDY study aims to generate a comprehensive understanding of how metabolic signatures in blood are affected in prediabetic autoimmunity and diabetes.
Institute:University of California, Davis
Department:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:451 Health Sci Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Publications:Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study. DOI: https://doi.org/10.1002/dmrr.2510

Subject:

Subject ID:SU001713
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 Sex cc
SA1384145859042Female 1
SA1384153058314Female 1
SA1384165856986Female 1
SA1384175853353Female 1
SA1384185833501Female 1
SA1384195881550Female 1
SA1384201441952Female 1
SA1384211440464Female 1
SA1384225920083Female 1
SA1384235890910Female 1
SA1384245888748Female 1
SA1384255823744Female 1
SA1384263058002Female 1
SA1384275802827Female 1
SA1384285744753Female 1
SA1384295747026Female 1
SA1384305735335Female 1
SA1384311464579Female 1
SA1384325719284Female 1
SA1384331459636Female 1
SA1384345748236Female 1
SA1384355799392Female 1
SA1384365929661Female 1
SA1384371749829Female 1
SA1384385764363Female 1
SA1384395758327Female 1
SA1384403070881Female 1
SA1384415937099Female 1
SA1384426108289Female 1
SA1384431762499Female 1
SA1384446069707Female 1
SA1384451761413Female 1
SA1384466068160Female 1
SA1384473026107Female 1
SA1384483022385Female 1
SA1384496227199Female 1
SA1384503002958Female 1
SA1384513003496Female 1
SA1384523020430Female 1
SA1384531419543Female 1
SA1384543034247Female 1
SA1384553040159Female 1
SA1384566009971Female 1
SA1384576013917Female 1
SA1384586003895Female 1
SA1384595981859Female 1
SA1384605944301Female 1
SA1384613045996Female 1
SA1384626026385Female 1
SA1384636052997Female 1
SA1384646052360Female 1
SA1384651758831Female 1
SA1384663040683Female 1
SA1384675707217Female 1
SA1384685689310Female 1
SA1384695388550Female 1
SA1384701496226Female 1
SA1384713141815Female 1
SA1384725351783Female 1
SA1384735350602Female 1
SA1384743132867Female 1
SA1384755439264Female 1
SA1384765488705Female 1
SA1384775498942Female 1
SA1384783113249Female 1
SA1384795472378Female 1
SA1384805455733Female 1
SA1384813164464Female 1
SA1384825344013Female 1
SA1384835306564Female 1
SA1384845315411Female 1
SA1384853188799Female 1
SA1384865298758Female 1
SA1384873198736Female 1
SA1384885324471Female 1
SA1384895330348Female 1
SA1384905343104Female 1
SA1384915336565Female 1
SA1384925334628Female 1
SA1384935333989Female 1
SA1384945507594Female 1
SA1384955523952Female 1
SA1384965615872Female 1
SA1384975640202Female 1
SA1384981478194Female 1
SA1384993089317Female 1
SA1385001479372Female 1
SA1385015656133Female 1
SA1385023077617Female 1
SA1385035681681Female 1
SA1385045687528Female 1
SA1385055681341Female 1
SA1385065680147Female 1
SA1385075678529Female 1
SA1385085596845Female 1
SA1385095580280Female 1
SA1385105527715Female 1
SA1385115537117Female 1
SA1385121488622Female 1
SA1385135524938Female 1
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Collection:

Collection ID:CO001706
Collection Summary:Plasma was obtained from human whole blood every 3 months up until 48 months; after 48 months, plasma was collected every 3 to 6 months depending on antibody status.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR001726
Treatment Summary:n/a

Sample Preparation:

Sampleprep ID:SP001719
Sampleprep Summary:See attached protocol.

Combined analysis:

Analysis ID AN002673 AN002674
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 6530 Agilent 6550
Column Waters Acquity CSH C18 (100 x 2.1mm,1.7um) Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH001967
Chromatography Summary:10,000 mass resolution for ESI(+) on an Agilent 6530 QTOF MS
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001968
Chromatography Summary:20,000 mass resolution for ESI(–) on an Agilent 6550 QTOF MS
Instrument Name:Agilent 6550
Column Name:Waters Acquity CSH C18 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002472
Analysis ID:AN002673
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:See "Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf"
Ion Mode:POSITIVE
  
MS ID:MS002473
Analysis ID:AN002674
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:See "Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf"
Ion Mode:NEGATIVE
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