Summary of study ST001386

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 IDST001386
Study TitleTEDDY Metabolomics Study
Study SummaryPrimary metabolites were quantified in human plasma from the 1:3 matched TEDDY case-control subjects. Information on the nested case-control study design can found in: Biomarker discovery study design for type 1 diabetes in The Environmental Determinants of Diabetes in the Young (TEDDY) study. 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. Diabetes/Metabolism Research and Reviews. Epub 2013 December 15. doi: 10.1002/dmrr.2510 (PubMed ID: 24339168). Primary metabolites were extracted from 30 µl plasma aliquots by adding 1 ml of a carefully degassed -20 °C cold isopropanol/acetonitrile/water mixture (3:3:2, v/v/v) for 5 min at 4 °C which simultaneously precipitates proteins. After centrifugation, half of the extract was dried and cleaned up from triglycerides by a 50% acetonitrile mixture. After drying, internal standards were added as C08-C30 fatty acid methyl esters in chloroform as retention index markers (Kind et. al, 2009). Primary metabolites were derivatized by methoximation and trimethylsilylation. Primary metabolites were analyzed by cold injection/automatic liner exchange gas chromatography time-of- flight mass spectrometry (CIS/ALEX GC-TOF MS) (Fiehn et. al, 2008). In order to limit buildup of involatile material in the GC system and to prevent any carry over, an automatic liner exchange with multi-baffled liners and cold injection procedures was used instead of classic hot injections into standard s/sl liners. Multi-baffled inert glass liners were used because classic glass wool liners might hamper derivatization of amino groups for amino acid analysis. Robotic derivatization was further used to control reaction times (Ji et. al, 2011); and GC-columns were employed with integrated 10 meter guard columns, which could cut multiple times in 10 cm increments whenever quality control samples determined out-of-control situations. A temperature of 280 °C was determined to be the optimum transfer line temperature at which even higher-boiling compounds did not show tailing effects and at which the electron ionization filaments could still be operated at their optimal temperature of 250 °C and -70 eV. The mass spectrometer was operated using daily mass calibration auto-tuning using FC43 (perfluorotributyl-amine) and acquired 17 spectra per second and 1850-1950 V detector voltage. This high spectral acquisition rate was necessary to obtain enough data for mass spectral deconvolution of co-eluting compounds. Under these conditions, the system was around 10-times more sensitive than classic quadrupole GC-MS instruments and also clearly outperformed GC-triple quadrupole mass spectrometers. For select compounds, even lower limits of detection were achieved than for optimized MRM conditions in UPLC-QTRAP MS analysis. Around 144 unique metabolites were detectable in blood plasma (Fiehn & Kind, 2007); in addition to 221 unidentified compounds that were captured in the BinBase database system and hence, were comparable across studies. References: 1) Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S, Fiehn O: FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 2009, 81(24):10038-10048. 2) Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau B: Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J 2008, 53(4):691-704. 3) Ji Y, Hebbring S, Zhu H, Jenkins GD, Biernacka J, Snyder K, Drews M, Fiehn O, Zeng Z, Schaid D et al: Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clin Pharmacol Ther 2011, 89(1):97-104. 4) Fiehn O, Kind T: Metabolite profiling in blood plasma. Methods Mol Biol 2007, 358:3-17. An explanation of the study design variables are explained in detail in a data dictionary provided in the raw data download section.
Institute
University of South Florida
LaboratoryUC Davis Genome Center
Last NameKrischer
First NameJeffrey
Address3650 Spectrum Blvd, Tampa, FL 33612
EmailTEDDYDataPlatform@epi.usf.edu
Phone8133969512
Submit Date2017-05-19
Publicationsdoi: 10.2337/db19-0756. Epub 2020 Feb 6. Longitudinal Metabolome-Wide Signals Prior to the Appearance of a First Islet Autoantibody in Children Participating in the TEDDY Study
Analysis Type DetailGC-MS
Release Date2020-06-30
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:SU001460
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Sex cc
SA1015404113970Female 1
SA1015411234699Female 1
SA1015424661659Female 1
SA1015439879061Female 1
SA1015448061139Female 1
SA1015459794821Female 1
SA1015466585218Female 1
SA1015474593901Female 1
SA1015488105863Female 1
SA1015497571450Female 1
SA1015503872232Female 1
SA1015516470191Female 1
SA1015528270491Female 1
SA1015539761395Female 1
SA1015548932916Female 1
SA1015554900146Female 1
SA1015564923530Female 1
SA1015571994496Female 1
SA1015588772680Female 1
SA1015596528448Female 1
SA1015606312149Female 1
SA1015612930114Female 1
SA1015628307869Female 1
SA1015634185183Female 1
SA1015644008614Female 1
SA1015651641296Female 1
SA1015663811553Female 1
SA1015678479924Female 1
SA1015684966900Female 1
SA1015691822339Female 1
SA1015703750709Female 1
SA1015714797006Female 1
SA1015723947734Female 1
SA1015739322822Female 1
SA1015742991482Female 1
SA1015756650490Female 1
SA1015767591497Female 1
SA1015772500142Female 1
SA1015784475881Female 1
SA1015795298758Female 1
SA1015803384613Female 1
SA1015812436180Female 1
SA1015828934854Female 1
SA1015838020841Female 1
SA1015841608840Female 1
SA1015851633736Female 1
SA1015866641833Female 1
SA1015879768263Female 1
SA1015882298411Female 1
SA1015894309543Female 1
SA1015906829359Female 1
SA1015912810427Female 1
SA1015929200876Female 1
SA1015931896080Female 1
SA1015946561333Female 1
SA1015955056601Female 1
SA1015965334628Female 1
SA1015974832393Female 1
SA1015987586161Female 1
SA1015996999355Female 1
SA1016005890910Female 1
SA1016019038259Female 1
SA1016029306593Female 1
SA1016039209559Female 1
SA1016049010968Female 1
SA1016054989189Female 1
SA1016061608202Female 1
SA1016074437835Female 1
SA1016083976328Female 1
SA1016099003755Female 1
SA1016107328445Female 1
SA1016112957601Female 1
SA1016123939919Female 1
SA1016133861023Female 1
SA1016146679688Female 1
SA1016154393791Female 1
SA1016169266312Female 1
SA1016174783563Female 1
SA1016187628496Female 1
SA1016195243390Female 1
SA1016207623738Female 1
SA1016212718088Female 1
SA1016227901886Female 1
SA1016232442664Female 1
SA1016244172618Female 1
SA1016257658525Female 1
SA1016262230682Female 1
SA1016275333989Female 1
SA1016281100710Female 1
SA1016292168560Female 1
SA1016306891740Female 1
SA1016311022719Female 1
SA1016325719284Female 1
SA1016334281457Female 1
SA1016341280961Female 1
SA1016351369777Female 1
SA1016361849327Female 1
SA1016374292078Female 1
SA1016385833501Female 1
SA1016397403674Female 1
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Collection:

Collection ID:CO001455
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:Plasma

Treatment:

Treatment ID:TR001475
Treatment Summary:n/a

Sample Preparation:

Sampleprep ID:SP001468
Sampleprep Summary:Blood plasma or serum is extracted following the protocols published e.g. in Fiehn et al. PLoS ONE (2010) e15234. 30 ?L aliquots are extracted by 1 mL of degassed acetonitrile : isopropanol : water (3:3:2,v/v/v ) at –20°C, centrifuged and decanted with subsequent evaporation of the solvent to complete dryness. A clean-up step with acetonitrile/water (1:1) removes membrane lipids and triglycerides. The cleaned extract is aliquoted into two equal portions and the supernatant is dried down again. Internal standards C08-C30 FAMEs are added and the sample is derivatized by methoxyamine hydrochloride in pyridine and subsequently by N-methyl-N-trimethylsilyltrifluoroacetamide for trimethylsilylation of acidic protons.

Combined analysis:

Analysis ID AN002314
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus IV GC
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode UNSPECIFIED
Units peak heights

Chromatography:

Chromatography ID:CH001701
Instrument Name:Leco Pegasus IV GC
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002157
Analysis ID:AN002314
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:See protocol.
Ion Mode:UNSPECIFIED
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