Summary of Study ST002681

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 PR001666. The data can be accessed directly via it's Project DOI: 10.21228/M8C13S 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 IDST002681
Study TitleNon-T2D vs T2D
Study SummaryPlasma samples from Senegalese individuals with T2D (n=31) or without T2D (n=34) were compared using mass-spectrometry-based metabolomics analyses.
Institute
University of Colorado Anschutz Medical Campus
Last NameNemkov
First NameTravis
Address12801 E 17th Avenue, RC-1 South, Rm 9403G, Aurora, CO, 80045, USA
Emailtravis.nemkov@cuanschutz.edu
Phone303-724-3253
Submit Date2023-04-25
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-10-26
Release Version1
Travis Nemkov Travis Nemkov
https://dx.doi.org/10.21228/M8C13S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001666
Project DOI:doi: 10.21228/M8C13S
Project Title:Metabolic profile of individuals with and without type 2 diabetes from sub-Saharan Africa
Project Summary:Epidemiological data predicts that Sub-Saharan Africa will have the largest increase in type 2 diabetes (T2D) prevalence over the next two decades. Metabolomics studies have identified biomarkers that could improve T2D diagnosis and follow-up. However, no studies have characterized the metabolome of people from Sub-Saharan Africa. Plasma samples from Senegalese individuals with T2D (n=31) or without T2D (n=34) were compared using measures of oxidative stress damage and plasma antioxidant enzyme activity, and mass-spectrometry-based lipidomics and metabolomics analyses. Results showed that glucose, lactate, and TCA metabolites (fumarate, malate, and succinate) were increased in the T2D group, suggesting alterations in glycolysis and mitochondrial dysfunction. Several amino acids (leucine, isoleucine, valine, and tryptophan) and long-to very-long-chain fatty acids were higher in the T2D group. Finally, elevated levels of ketone bodies and acylcarnitines were observed along with increased levels of oxidative stress damage and anti-oxidant activity. In conclusion, the T2D group exhibited modifications in metabolites previously shown to be associated with T2D risk in populations from other areas of the world. Future studies should seek to test whether these metabolites could be used as predictors for T2D-related complications in people from Sub-Saharan Africa.
Institute:University of Colorado Anschutz Medical Campus
Last Name:Nemkov
First Name:Travis
Address:12801 E 17th Avenue, RC-1 South, Rm 9121, Aurora, CO, 80045, USA
Email:travis.nemkov@cuanschutz.edu
Phone:303-724-3253

Subject:

Subject ID:SU002783
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
SA265552Control_FAKA+Control
SA265553Control_FAAH+Control
SA265554Control_EMYA+Control
SA265555Control_FAND+Control
SA265556Control_HABA+Control
SA265557Control_IBGA+Control
SA265558Control_HOLE+Control
SA265559Control_DOMA+Control
SA265560Control_DIEM+Control
SA265561Control_BACO+Control
SA265562Control_BABI+Control
SA265563Control_AMDI+Control
SA265564Control_BADA+Control
SA265565Control_CECA+Control
SA265566Control_KHGU+Control
SA265567Control_COMA+Control
SA265568Control_DIMA31+Control
SA265569Control_MAMB+Control
SA265570Control_SAAL+Control
SA265571Control_SAAD+Control
SA265572Control_RAFA+Control
SA265573Control_SACA23+Control
SA265574Control_SADI+Control
SA265575Control_SESO+Control
SA265576Control_SALL+Control
SA265577Control_PAMA+Control
SA265578Control_NZFE+Control
SA265579Control_MEPA+Control
SA265580Control_MBKH+Control
SA265581Control_MOKE+Control
SA265582Control_NDFA25+Control
SA265583Control_NGEU+Control
SA265584Control_NDGU23+Control
SA265585Control_AKLA-Control
SA265586Control_AKLA+Control
SA265587Control_NDFA25-Control
SA265588Control_NDGU23-Control
SA265589Control_MOKE-Control
SA265590Control_MEPA-Control
SA265591Control_MAMB-Control
SA265592Control_MBKH-Control
SA265593Control_NGEU-Control
SA265594Control_NZFE-Control
SA265595Control_SACA23-Control
SA265596Control_SADI-Control
SA265597Control_SAAL-Control
SA265598Control_SAAD-Control
SA265599Control_PAMA-Control
SA265600Control_RAFA-Control
SA265601Control_IBGA-Control
SA265602Control_HOLE-Control
SA265603Control_CECA-Control
SA265604Control_COMA-Control
SA265605Control_BADA-Control
SA265606Control_BACO-Control
SA265607Control_AMDI-Control
SA265608Control_BABI-Control
SA265609Control_DIEM-Control
SA265610Control_DIMA31-Control
SA265611Control_FAND-Control
SA265612Control_HABA-Control
SA265613Control_FAKA-Control
SA265614Control_FAAH-Control
SA265615Control_DOMA-Control
SA265616Control_EMYA-Control
SA265617Control_SALL-Control
SA265618Control_KHGU-Control
SA265619Control_SESO-Control
SA265620T2D_GUOU+T2D
SA265621T2D_FAOU+T2D
SA265622T2D_GUSA+T2D
SA265623T2D_LEWA+T2D
SA265624T2D_MADI52+T2D
SA265625T2D_FAAS+T2D
SA265626T2D_KAAD+T2D
SA265627T2D_DIKH+T2D
SA265628T2D_DAFA60+T2D
SA265629T2D_CODI+T2D
SA265630T2D_DIDA+T2D
SA265631T2D_DIFA+T2D
SA265632T2D_MBPA+T2D
SA265633T2D_DIFA37+T2D
SA265634T2D_DSMA+T2D
SA265635T2D_MOMB+T2D
SA265636T2D_SASE+T2D
SA265637T2D_SAMO11+T2D
SA265638T2D_SODA+T2D
SA265639T2D_SOFA+T2D
SA265640T2D_DAFA60-T2D
SA265641T2D_THAN+T2D
SA265642T2D_SAKH+T2D
SA265643T2D_SADI+T2D
SA265644T2D_NDMO+T2D
SA265645T2D_NDFA+T2D
SA265646T2D_NDND+T2D
SA265647T2D_NDOU+T2D
SA265648T2D_NIIB+T2D
SA265649T2D_NDPA+T2D
SA265650T2D_CAFA+T2D
SA265651T2D_BASA+T2D
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Collection:

Collection ID:CO002776
Collection Summary:Blood was drawn into fluoride tubes for glucose measurement, heparin tubes for lipid measurement, and EDTA tubes for HbA1c and metabolomics analyses. Plasma was isolated and stored at -80C until analysis.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002792
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002789
Sampleprep Summary:Prior to LC-MS analysis, 10ul of plasma was resuspended in 9 volumes of pre-chilled (-20°C) methanol:acetonitrile:water (5:3:2, v:v) and vortexed continuously for 30 min at 4°C. Insoluble material was removed by centrifugation at 18,000 g for 10 min at 4°C and supernatants were isolated for metabolomics analysis by UHPLC-MS.

Combined analysis:

Analysis ID AN004353 AN004354
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Phenomenex Kinetex C18 (100 x 2.1mm,1.7um) Phenomenex Kinetex C18 (100 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units AU AU

Chromatography:

Chromatography ID:CH003259
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:0-0.5min 5% B; 1.1min 95% B; 2.75min 95%B; 3min 5%B; 5min 5%B
Flow Rate:0.45
Solvent A:0.1% formic acid in water
Solvent B:0.1% formic acid in acetonitrile
Chromatography Type:Reversed phase
  
Chromatography ID:CH003260
Instrument Name:Thermo Vanquish
Column Name:Phenomenex Kinetex C18 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:0-0.5min 5% B; 1.1min 95% B; 2.75min 95%B; 3min 5%B; 5min 5%B
Flow Rate:0.45
Solvent A:5% acetonitrile 1mM ammonium acetate
Solvent B:95% acetonitrile 1mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS004100
Analysis ID:AN004353
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 microscans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)
Ion Mode:POSITIVE
  
MS ID:MS004101
Analysis ID:AN004354
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 microscans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)
Ion Mode:NEGATIVE
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