Summary of Study ST003636

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 PR002243. The data can be accessed directly via it's Project DOI: 10.21228/M8PR8Q This work is supported by NIH grant, U2C- DK119886.

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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 IDST003636
Study TitleIndividual glycemic responses to carbohydrates vary and reflect underlying metabolic physiology (metabolomics)
Study SummaryWe measured PPGRs using continuous glucose monitoring (CGM) in 55 well-phenotyped participants challenged with seven different carbohydrates administered in replicate under standardized conditions. Plasma sample were collected at baseline visit for metabolomics. The ClinicalTrials.gov registration identifier is NCT03919877.
Institute
Stanford University
Last NameMichael
First NameSnyder
Address300 Pasteur Drive, M-344A Stanford, California 94305
Emailmpsnyder@stanford.edu
Phone(650) 723-4668
Submit Date2024-11-17
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-01-14
Release Version1
Snyder Michael Snyder Michael
https://dx.doi.org/10.21228/M8PR8Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002243
Project DOI:doi: 10.21228/M8PR8Q
Project Title:Individual glycemic responses to carbohydrates vary and reflect underlying metabolic physiology
Project Summary:Elevated postprandial glycemic responses (PPGRs) are associated with type 2 diabetes and cardiovascular disease. PPGRs to the same foods have been shown to vary between individuals, but the systematic characterization of the underlying physiologic and molecular basis is lacking. We measured PPGRs using continuous glucose monitoring (CGM) in 55 well-phenotyped participants challenged with seven different carbohydrates administered in replicate under standardized conditions. We also measured the effects of preloading a rice meal with fiber, protein, or fat (“mitigators”). To examine the physiologic and molecular basis for inter-individual PPGR differences, we performed gold-standard metabolic tests and multi-omics profiling. We discovered: 1. Postprandial glycemic responses (PPGRs) to different standardized carbohydrate meals vary between individuals. 2. Individuals’ PPGRs are associated with their metabolic phenotypes, including insulin resistance. 3. Individual’s PPGRs can be reduced in magnitude and delayed by premeal mitigators which is associated with their metabolic phenotypes. 4. Individuals can be stratified by their PPGRs to different carbohydrate meals, and PPGR subtypes have distinct metabolic profiles and multi-omics patterns. 5. Individuals’ metabolic phenotype can be inferred from both food-specific PPGRs and baseline omics.
Institute:Stanford University
Department:Genetics
Laboratory:Michael P. Snyder
Last Name:Snyder
First Name:Michael
Address:300 Pasteur Drive, M-344A Stanford, California 94305
Email:mpsnyder@stanford.edu
Phone:(650) 723-4668
Funding Source:NIH

Subject:

Subject ID:SU003766
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Sample source Time
SA393902XB21_4plasma Baseline
SA393903XB107_5plasma Baseline
SA393904XB95_3plasma Baseline
SA393905XB94_2plasma Baseline
SA393906XB115_1plasma Baseline
SA393907XB107_4plasma Baseline
SA393908XB79_6plasma Baseline
SA393909XB14_3plasma Baseline
SA393910XB76_1plasma Baseline
SA393911XB20_5plasma Baseline
SA393912XB65_1plasma Baseline
SA393913XB21_5plasma Baseline
SA393914XB6_2plasma Baseline
SA393915XB115_2plasma Baseline
SA393916XB38_5plasma Baseline
SA393917XB21_3plasma Baseline
SA393918XB1_3plasma Baseline
SA393919XB59_3plasma Baseline
SA393920XB111_3plasma Baseline
SA393921XB100_4plasma Baseline
SA393922XB111_2plasma Baseline
SA393923XB107_3plasma Baseline
SA393924XB22_1plasma Baseline
SA393925XB33_4plasma Baseline
SA393926XB114_1plasma Baseline
SA393927XB59_4plasma Baseline
SA393928XB45_2plasma Baseline
SA393929XB97_1plasma Baseline
SA393930XB97_3plasma Baseline
SA393931XB25_2plasma Baseline
SA393932XB115_4plasma Baseline
SA393933XB68_5plasma Baseline
SA393934XB22_2plasma Baseline
SA393935XB20_6plasma Baseline
SA393936XB89_4plasma Baseline
SA393937XB94_3plasma Baseline
SA393938XB114_3plasma Baseline
SA393939XB79_7plasma Baseline
SA393940XB112_2plasma Baseline
SA393941XB25_1plasma Baseline
SA393942XB114_2plasma Baseline
SA393943XB100_5plasma Baseline
SA393944XB65_2plasma Baseline
SA393945XB1_5plasma Baseline
SA393946XB43_3plasma Baseline
SA393947XB115_3plasma Baseline
SA393948XB1_4plasma Baseline
SA393949XB2_2plasma Baseline
SA393950XB97_2plasma Baseline
SA393951XB43_2plasma Baseline
SA393952XB43_1plasma Baseline
SA393953XB68_4plasma Baseline
SA393954XB6_3plasma Baseline
SA393955XB89_3plasma Baseline
SA393956XB20_4plasma Baseline
SA393957XB59_1plasma Baseline
SA393958XB45_1plasma Baseline
SA393959XB38_1plasma Baseline
SA393960XB79_3plasma Baseline
SA393961XB54_1plasma Baseline
SA393962XB79_2plasma Baseline
SA393963XB20_2plasma Baseline
SA393964XB111_1plasma Baseline
SA393965XB59_2plasma Baseline
SA393966XB32_1plasma Baseline
SA393967XB95_2plasma Baseline
SA393968XB44_1plasma Baseline
SA393969XB20_1plasma Baseline
SA393970XB24_1plasma Baseline
SA393971XB79_1plasma Baseline
SA393972XB1_1plasma Baseline
SA393973XB101_1plasma Baseline
SA393974XB70_3plasma Baseline
SA393975XB14_2plasma Baseline
SA393976XB95_1plasma Baseline
SA393977XB18_1plasma Baseline
SA393978XB100_2plasma Baseline
SA393979XB70_2plasma Baseline
SA393980XB70_1plasma Baseline
SA393981XB68_1plasma Baseline
SA393982XB2_1plasma Baseline
SA393983XB14_1plasma Baseline
SA393984XB100_1plasma Baseline
SA393985XB89_1plasma Baseline
SA393986XB68_2plasma Baseline
SA393987XB1_2plasma Baseline
SA393988XB100_3plasma Baseline
SA393989XB79_5plasma Baseline
SA393990XB38_4plasma Baseline
SA393991XB94_1plasma Baseline
SA393992XB20_3plasma Baseline
SA393993XB68_3plasma Baseline
SA393994XB34_1plasma Baseline
SA393995XB6_1plasma Baseline
SA393996XB107_2plasma Baseline
SA393997XB62_1plasma Baseline
SA393998XB21_2plasma Baseline
SA393999XB38_3plasma Baseline
SA394000XB33_3plasma Baseline
SA394001XB21_1plasma Baseline
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Collection:

Collection ID:CO003759
Collection Summary:Participants underwent evaluations, screening tests, and metabolic tests at the CTRU after an overnight fast. During the screening and the omics visits, stool, urine, peripheral blood mononuclear cells (PBMC), plasma, and serum samples were collected. Some individuals had multiple omics visits to monitor omics changes throughout the study.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003775
Treatment Summary:Baseline sample no treatment.
Human Fasting:Yes

Sample Preparation:

Sampleprep ID:SP003773
Sampleprep Summary:Metabolites and complex lipids were extracted using a biphasic separation with cold methyl tert-butyl ether (MTBE), methanol, and water in the deep well plate format.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN005969 AN005970 AN005971 AN005972
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Q Exactive HF Thermo Q Exactive HF Thermo Q Exactive Thermo Q Exactive
Column Merck ZIC-HILIC column (100 x 2.1 mm, 3.5μm, 200Å) Merck ZIC-HILIC column (100 x 2.1 mm, 3.5μm, 200Å) Agilent Zorbax SBaq column (50 x 2.1 mm, 1.7μm, 100Å) Agilent Zorbax SBaq column (50 x 2.1 mm, 1.7μm, 100Å)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units intensity intensity intensity intensity

Chromatography:

Chromatography ID:CH004535
Instrument Name:Thermo Q Exactive HF
Column Name:Merck ZIC-HILIC column (100 x 2.1 mm, 3.5μm, 200Å)
Column Temperature:40℃
Flow Gradient:Details in the attachment
Flow Rate:0.5 mL/min
Internal Standard:Yes
Solvent A:50% Acetonitrile/50% Water; 10mM Ammonium acetate
Solvent B:95% Acetonitrile/5% Water;10 mM ammonium acetate
Chromatography Type:HILIC
  
Chromatography ID:CH004536
Instrument Name:Thermo Q Exactive
Column Name:Agilent Zorbax SBaq column (50 x 2.1 mm, 1.7μm, 100Å)
Column Temperature:60℃
Flow Gradient:Details in the attachment
Flow Rate:0.6 mL/min
Internal Standard:Yes
Solvent A:100% Water; 0.06% Acetic acid
Solvent B:100% Methanol; 0.06% Acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005682
Analysis ID:AN005969
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS/MS data were acquired on quality control samples (QC) consisting of an equimolar mixture of all samples in the study. HILIC experiments were performed using a ZIC-HILIC column 2.1 x 100mm, 3.5μm, 200Å (Merck Millipore, Darmstadt, Germany) and mobile phase solvents consisting of 10mM ammonium acetate in 50/50 acetonitrile/water (A) and 10 mM ammonium acetate in 95/5 acetonitrile/water (B). Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that did not show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Intensity drift was corrected using the SERRF (systematic error removal using random forest) method. Data from each mode were merged and metabolic features were annotated as follows. Peak annotation was first performed by matching experimental m/z, retention time, and MS/MS spectra to an in-house library of analytical-grade standards. Details in the protocol.
Ion Mode:POSITIVE
  
MS ID:MS005683
Analysis ID:AN005970
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS/MS data were acquired on quality control samples (QC) consisting of an equimolar mixture of all samples in the study. HILIC experiments were performed using a ZIC-HILIC column 2.1 x 100mm, 3.5μm, 200Å (Merck Millipore, Darmstadt, Germany) and mobile phase solvents consisting of 10mM ammonium acetate in 50/50 acetonitrile/water (A) and 10 mM ammonium acetate in 95/5 acetonitrile/water (B). Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that did not show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Intensity drift was corrected using the SERRF (systematic error removal using random forest) method. Data from each mode were merged and metabolic features were annotated as follows. Peak annotation was first performed by matching experimental m/z, retention time, and MS/MS spectra to an in-house library of analytical-grade standards. Details in the protocol.
Ion Mode:NEGATIVE
  
MS ID:MS005684
Analysis ID:AN005971
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS/MS data were acquired on quality control samples (QC) consisting of an equimolar mixture of all samples in the study. RPLC experiments were performed using a Zorbax SBaq column 2.1 x 50mm, 1.7μm, 100Å (Agilent Technologies, Palo Alto, CA) and mobile phase solvents consisting of 0.06% acetic acid in water (A) and 0.06% acetic acid in methanol (B). Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that did not show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Intensity drift was corrected using the SERRF (systematic error removal using random forest) method. Data from each mode were merged and metabolic features were annotated as follows. Peak annotation was first performed by matching experimental m/z, retention time, and MS/MS spectra to an in-house library of analytical-grade standards. Details in the protocol.
Ion Mode:POSITIVE
  
MS ID:MS005685
Analysis ID:AN005972
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS/MS data were acquired on quality control samples (QC) consisting of an equimolar mixture of all samples in the study. RPLC experiments were performed using a Zorbax SBaq column 2.1 x 50mm, 1.7μm, 100Å (Agilent Technologies, Palo Alto, CA) and mobile phase solvents consisting of 0.06% acetic acid in water (A) and 0.06% acetic acid in methanol (B). Data from each mode were independently analyzed using Progenesis QI software (v2.3) (Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and those that did not show sufficient linearity upon dilution in QC samples (r<0.6) were discarded. Only metabolic features present in >2/3 of the samples were kept for further analysis. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Intensity drift was corrected using the SERRF (systematic error removal using random forest) method. Data from each mode were merged and metabolic features were annotated as follows. Peak annotation was first performed by matching experimental m/z, retention time, and MS/MS spectra to an in-house library of analytical-grade standards. Details in the protocol.
Ion Mode:NEGATIVE
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