Summary of Study ST002200

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 PR001403. The data can be accessed directly via it's Project DOI: 10.21228/M8C99T 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 IDST002200
Study TitleHuman Trisome Project Plasma Metabolomics v1
Study SummaryAnalysis of metabolite relative abundance in blood plasma from 316 individuals with trisomy 21 (T21, Down syndrome) and 103 euploid controls. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/
Institute
University of Colorado Denver
LaboratoryPIs - Joaquin Espinosa and Angelo D'Alessandro
Last NameHaines
First NameJulie
Address12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Emailjulie.haines@cuanschutz.edu
Phone3037243339
Submit Date2022-06-15
Num Groups2
Total Subjects419
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-06-15
Release Version1
Julie Haines Julie Haines
https://dx.doi.org/10.21228/M8C99T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001403
Project DOI:doi: 10.21228/M8C99T
Project Title:Human Trisome Project Plasma Metabolomics v1
Project Summary:Analysis of metabolite relative abundance in blood plasma from 316 individuals with trisomy 21 (T21, Down syndrome) and 103 euploid controls. This dataset focuses on hydrophilic metabolites and oxylipins and is part of the Human Trisome Project (HTP, http://www.trisome.org/) run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. This data is generated from samples matched at the blood draw to multiple omics datasets including proteomics, cytokine profiling, RNA-seq, and mass cytometry. The HTP is an in-depth study of people with Down syndrome using the latest technologies in precision medicine. The goal of the HTP is to enable advanced therapeutic approaches to enhance the quality of life and extend the lifespan of those with trisomy 21 through the study of the co-occurring conditions of Down syndrome. The HTP leverages a multidisciplinary team of biomedical researchers, clinicians and data scientists located across multiple departments, divisions, institutes and centers at the University of Colorado who work together toward a single goal: to decipher why people with trisomy 21 have a different disease spectrum, being predisposed to some medical conditions while being protected from others. The HTP Biobank provides de-identified samples and clinical information to collaborators that are necessary for investigations that advance our understanding of several co-occurring medical conditions in Down syndrome. Studies using samples and data from the HTP Biobank are enabling the development of novel diagnostics and therapeutic approaches, serving not only individuals with Down syndrome, but also the billions worldwide affected by conditions that commonly co-occur in Down syndrome. This collaborative and multi-disciplinary model allows for one of the largest and most comprehensive studies of individuals with Down syndrome to date, including extensive characterization at the clinical, physiological, cellular and molecular levels.
Institute:University of Colorado Denver
Laboratory:PIs - Joaquin Espinosa and Angelo D'Alessandro
Last Name:Haines
First Name:Julie
Address:12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Email:julie.haines@cuanschutz.edu
Phone:3037243339

Subject:

Subject ID:SU002286
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 Group
SA210738H-324D21
SA210739H-325D21
SA210740H-323D21
SA210741H-322D21
SA210742H-321D21
SA210743H-326D21
SA210744H-327D21
SA210745H-339D21
SA210746H-330D21
SA210747H-329D21
SA210748H-328D21
SA210749H-320D21
SA210750H-315D21
SA210751H-307D21
SA210752H-309D21
SA210753H-302D21
SA210754H-301D21
SA210755H-300D21
SA210756H-310D21
SA210757H-311D21
SA210758H-340D21
SA210759H-314D21
SA210760H-313D21
SA210761H-312D21
SA210762H-316D21
SA210763H-342D21
SA210764H-371D21
SA210765H-374D21
SA210766H-370D21
SA210767H-369D21
SA210768H-367D21
SA210769H-388D21
SA210770H-389D21
SA210771H-010D21
SA210772H-419D21
SA210773H-398D21
SA210774H-392D21
SA210775H-365D21
SA210776H-357D21
SA210777H-347D21
SA210778H-348D21
SA210779H-346D21
SA210780H-343D21
SA210781H-299D21
SA210782H-349D21
SA210783H-351D21
SA210784H-355D21
SA210785H-354D21
SA210786H-353D21
SA210787H-352D21
SA210788H-341D21
SA210789H-356D21
SA210790H-080D21
SA210791H-081D21
SA210792H-077D21
SA210793H-076D21
SA210794H-069D21
SA210795H-082D21
SA210796H-084D21
SA210797H-091D21
SA210798H-089D21
SA210799H-088D21
SA210800H-085D21
SA210801H-066D21
SA210802H-065D21
SA210803H-037D21
SA210804H-043D21
SA210805H-036D21
SA210806H-298D21
SA210807H-034D21
SA210808H-051D21
SA210809H-054D21
SA210810H-063D21
SA210811H-059D21
SA210812H-058D21
SA210813H-056D21
SA210814H-092D21
SA210815H-057D21
SA210816H-244D21
SA210817H-256D21
SA210818H-243D21
SA210819H-240D21
SA210820H-231D21
SA210821H-261D21
SA210822H-281D21
SA210823H-294D21
SA210824H-292D21
SA210825H-101D21
SA210826H-290D21
SA210827H-283D21
SA210828H-224D21
SA210829H-264D21
SA210830H-137D21
SA210831H-162D21
SA210832H-206D21
SA210833H-152D21
SA210834H-154D21
SA210835H-170D21
SA210836H-169D21
SA210837H-183D21
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Collection:

Collection ID:CO002279
Collection Summary:All study participants were enrolled in the Crnic Institute Human Trisome Project (HTP) under a study protocol approved by the Colorado Multiple Institutional Review Board (NCT02864108, see also www.trisome.org). Written informed consent was obtained from all study participants or their legal guardians. Data were generated from deidentified biospecimens and linked to demographics and clinical metadata for analysis. Peripheral blood samples were collected into BD Vacutainer K2 EDTA tubes (BD, Cat # 366643) and processed within 2 hrs of blood draw by centrifugation at 700 x g for 15 min to separate plasma, buffy coat (white blood cells, WBCs), and red blood cells (RBCs) which were aliquoted, flash-frozen, and stored at -80°C. Subsequent processing was carried out as described below, with aliquots selected to minimize freeze/thaw cycles.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002298
Treatment Summary:n/a

Sample Preparation:

Sampleprep ID:SP002292
Sampleprep Summary:Metabolite extraction: Samples were thawed on ice and 20 μL of sample was diluted in 480 μL of LC-MS grade cold methanol/acetonitrile/water (5:3:2). Samples were incubated at 4°C for 30 min with vigorous vortexing. Supernatants were clarified by centrifugation (10 min, 18,213 g, 4C) then 50 uL aliquots were transferred to autosampler vials. Lipid extraction: Samples were thawed on ice and 10 uL of sample was diluted in 90 uL of LC-MS grade cold methanol. Samples were briefly vortexed to mix then incubated for 30 min at -20C. Supernatants were clarified by centrifugation (10 min, 18,213 g, 4C) then 25 uL aliquots were transferred to autosampler vials and diluted with 25 uL of 10 mM ammonium acetate.

Combined analysis:

Analysis ID AN003600 AN003601 AN003602 AN003603
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um) Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode NEGATIVE POSITIVE NEGATIVE POSITIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH002660
Chromatography Summary:5 minute negative metabolites
Methods Filename:Merged_chromatography_methods_metabolites_and_lipids.docx
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002661
Chromatography Summary:5 minute positive metabolites
Methods Filename:Merged_chromatography_methods_metabolites_and_lipids.docx
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (150 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002662
Chromatography Summary:17 minute negative oxylipins
Methods Filename:Merged_chromatography_methods_metabolites_and_lipids.docx
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002663
Chromatography Summary:15 minute positive metabolites
Methods Filename:Merged_chromatography_methods_metabolites_and_lipids.docx
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY HSS T3 (150 x 2.1mm,1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003355
Analysis ID:AN003600
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database.
Ion Mode:NEGATIVE
  
MS ID:MS003356
Analysis ID:AN003601
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database.
Ion Mode:POSITIVE
  
MS ID:MS003357
Analysis ID:AN003602
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Resolution 70,000, scan range 150-1500 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database.
Ion Mode:NEGATIVE
  
MS ID:MS003358
Analysis ID:AN003603
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Resolution 70,000, scan range 150-1500 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database.
Ion Mode:POSITIVE
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