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.
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.
Study ID | ST003636 |
Study Title | Individual glycemic responses to carbohydrates vary and reflect underlying metabolic physiology (metabolomics) |
Study Summary | We 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 Name | Michael |
First Name | Snyder |
Address | 300 Pasteur Drive, M-344A Stanford, California 94305 |
mpsnyder@stanford.edu | |
Phone | (650) 723-4668 |
Submit Date | 2024-11-17 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2025-01-14 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
---|---|---|---|
SA393902 | XB21_4 | plasma | Baseline |
SA393903 | XB107_5 | plasma | Baseline |
SA393904 | XB95_3 | plasma | Baseline |
SA393905 | XB94_2 | plasma | Baseline |
SA393906 | XB115_1 | plasma | Baseline |
SA393907 | XB107_4 | plasma | Baseline |
SA393908 | XB79_6 | plasma | Baseline |
SA393909 | XB14_3 | plasma | Baseline |
SA393910 | XB76_1 | plasma | Baseline |
SA393911 | XB20_5 | plasma | Baseline |
SA393912 | XB65_1 | plasma | Baseline |
SA393913 | XB21_5 | plasma | Baseline |
SA393914 | XB6_2 | plasma | Baseline |
SA393915 | XB115_2 | plasma | Baseline |
SA393916 | XB38_5 | plasma | Baseline |
SA393917 | XB21_3 | plasma | Baseline |
SA393918 | XB1_3 | plasma | Baseline |
SA393919 | XB59_3 | plasma | Baseline |
SA393920 | XB111_3 | plasma | Baseline |
SA393921 | XB100_4 | plasma | Baseline |
SA393922 | XB111_2 | plasma | Baseline |
SA393923 | XB107_3 | plasma | Baseline |
SA393924 | XB22_1 | plasma | Baseline |
SA393925 | XB33_4 | plasma | Baseline |
SA393926 | XB114_1 | plasma | Baseline |
SA393927 | XB59_4 | plasma | Baseline |
SA393928 | XB45_2 | plasma | Baseline |
SA393929 | XB97_1 | plasma | Baseline |
SA393930 | XB97_3 | plasma | Baseline |
SA393931 | XB25_2 | plasma | Baseline |
SA393932 | XB115_4 | plasma | Baseline |
SA393933 | XB68_5 | plasma | Baseline |
SA393934 | XB22_2 | plasma | Baseline |
SA393935 | XB20_6 | plasma | Baseline |
SA393936 | XB89_4 | plasma | Baseline |
SA393937 | XB94_3 | plasma | Baseline |
SA393938 | XB114_3 | plasma | Baseline |
SA393939 | XB79_7 | plasma | Baseline |
SA393940 | XB112_2 | plasma | Baseline |
SA393941 | XB25_1 | plasma | Baseline |
SA393942 | XB114_2 | plasma | Baseline |
SA393943 | XB100_5 | plasma | Baseline |
SA393944 | XB65_2 | plasma | Baseline |
SA393945 | XB1_5 | plasma | Baseline |
SA393946 | XB43_3 | plasma | Baseline |
SA393947 | XB115_3 | plasma | Baseline |
SA393948 | XB1_4 | plasma | Baseline |
SA393949 | XB2_2 | plasma | Baseline |
SA393950 | XB97_2 | plasma | Baseline |
SA393951 | XB43_2 | plasma | Baseline |
SA393952 | XB43_1 | plasma | Baseline |
SA393953 | XB68_4 | plasma | Baseline |
SA393954 | XB6_3 | plasma | Baseline |
SA393955 | XB89_3 | plasma | Baseline |
SA393956 | XB20_4 | plasma | Baseline |
SA393957 | XB59_1 | plasma | Baseline |
SA393958 | XB45_1 | plasma | Baseline |
SA393959 | XB38_1 | plasma | Baseline |
SA393960 | XB79_3 | plasma | Baseline |
SA393961 | XB54_1 | plasma | Baseline |
SA393962 | XB79_2 | plasma | Baseline |
SA393963 | XB20_2 | plasma | Baseline |
SA393964 | XB111_1 | plasma | Baseline |
SA393965 | XB59_2 | plasma | Baseline |
SA393966 | XB32_1 | plasma | Baseline |
SA393967 | XB95_2 | plasma | Baseline |
SA393968 | XB44_1 | plasma | Baseline |
SA393969 | XB20_1 | plasma | Baseline |
SA393970 | XB24_1 | plasma | Baseline |
SA393971 | XB79_1 | plasma | Baseline |
SA393972 | XB1_1 | plasma | Baseline |
SA393973 | XB101_1 | plasma | Baseline |
SA393974 | XB70_3 | plasma | Baseline |
SA393975 | XB14_2 | plasma | Baseline |
SA393976 | XB95_1 | plasma | Baseline |
SA393977 | XB18_1 | plasma | Baseline |
SA393978 | XB100_2 | plasma | Baseline |
SA393979 | XB70_2 | plasma | Baseline |
SA393980 | XB70_1 | plasma | Baseline |
SA393981 | XB68_1 | plasma | Baseline |
SA393982 | XB2_1 | plasma | Baseline |
SA393983 | XB14_1 | plasma | Baseline |
SA393984 | XB100_1 | plasma | Baseline |
SA393985 | XB89_1 | plasma | Baseline |
SA393986 | XB68_2 | plasma | Baseline |
SA393987 | XB1_2 | plasma | Baseline |
SA393988 | XB100_3 | plasma | Baseline |
SA393989 | XB79_5 | plasma | Baseline |
SA393990 | XB38_4 | plasma | Baseline |
SA393991 | XB94_1 | plasma | Baseline |
SA393992 | XB20_3 | plasma | Baseline |
SA393993 | XB68_3 | plasma | Baseline |
SA393994 | XB34_1 | plasma | Baseline |
SA393995 | XB6_1 | plasma | Baseline |
SA393996 | XB107_2 | plasma | Baseline |
SA393997 | XB62_1 | plasma | Baseline |
SA393998 | XB21_2 | plasma | Baseline |
SA393999 | XB38_3 | plasma | Baseline |
SA394000 | XB33_3 | plasma | Baseline |
SA394001 | XB21_1 | plasma | Baseline |
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 |