Summary of Study ST003630
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 | ST003630 |
Study Title | Individual glycemic responses to carbohydrates vary and reflect underlying metabolic physiology (Lipidomics) |
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 | 2024-11-18 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2025-01-12 |
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: | SU003760 |
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 |
---|---|---|---|
SA393523 | XB21_4 | plasma | Baseline |
SA393524 | XB107_5 | plasma | Baseline |
SA393525 | XB95_3 | plasma | Baseline |
SA393526 | XB94_2 | plasma | Baseline |
SA393527 | XB115_1 | plasma | Baseline |
SA393528 | XB107_4 | plasma | Baseline |
SA393529 | XB79_6 | plasma | Baseline |
SA393530 | XB14_3 | plasma | Baseline |
SA393531 | XB76_1 | plasma | Baseline |
SA393532 | XB20_5 | plasma | Baseline |
SA393533 | XB65_1 | plasma | Baseline |
SA393534 | XB21_5 | plasma | Baseline |
SA393535 | XB6_2 | plasma | Baseline |
SA393536 | XB115_2 | plasma | Baseline |
SA393537 | XB38_5 | plasma | Baseline |
SA393538 | XB21_3 | plasma | Baseline |
SA393539 | XB1_3 | plasma | Baseline |
SA393540 | XB59_3 | plasma | Baseline |
SA393541 | XB111_3 | plasma | Baseline |
SA393542 | XB100_4 | plasma | Baseline |
SA393543 | XB111_2 | plasma | Baseline |
SA393544 | XB107_3 | plasma | Baseline |
SA393545 | XB22_1 | plasma | Baseline |
SA393546 | XB33_4 | plasma | Baseline |
SA393547 | XB114_1 | plasma | Baseline |
SA393548 | XB59_4 | plasma | Baseline |
SA393549 | XB45_2 | plasma | Baseline |
SA393550 | XB97_1 | plasma | Baseline |
SA393551 | XB97_3 | plasma | Baseline |
SA393552 | XB25_2 | plasma | Baseline |
SA393553 | XB115_4 | plasma | Baseline |
SA393554 | XB68_5 | plasma | Baseline |
SA393555 | XB22_2 | plasma | Baseline |
SA393556 | XB20_6 | plasma | Baseline |
SA393557 | XB89_4 | plasma | Baseline |
SA393558 | XB94_3 | plasma | Baseline |
SA393559 | XB114_3 | plasma | Baseline |
SA393560 | XB79_7 | plasma | Baseline |
SA393561 | XB112_2 | plasma | Baseline |
SA393562 | XB25_1 | plasma | Baseline |
SA393563 | XB114_2 | plasma | Baseline |
SA393564 | XB100_5 | plasma | Baseline |
SA393565 | XB65_2 | plasma | Baseline |
SA393566 | XB1_5 | plasma | Baseline |
SA393567 | XB43_3 | plasma | Baseline |
SA393568 | XB115_3 | plasma | Baseline |
SA393569 | XB1_4 | plasma | Baseline |
SA393570 | XB2_2 | plasma | Baseline |
SA393571 | XB97_2 | plasma | Baseline |
SA393572 | XB43_2 | plasma | Baseline |
SA393573 | XB43_1 | plasma | Baseline |
SA393574 | XB68_4 | plasma | Baseline |
SA393575 | XB6_3 | plasma | Baseline |
SA393576 | XB89_3 | plasma | Baseline |
SA393577 | XB20_4 | plasma | Baseline |
SA393578 | XB59_1 | plasma | Baseline |
SA393579 | XB45_1 | plasma | Baseline |
SA393580 | XB38_1 | plasma | Baseline |
SA393581 | XB79_3 | plasma | Baseline |
SA393582 | XB54_1 | plasma | Baseline |
SA393583 | XB79_2 | plasma | Baseline |
SA393584 | XB20_2 | plasma | Baseline |
SA393585 | XB111_1 | plasma | Baseline |
SA393586 | XB59_2 | plasma | Baseline |
SA393587 | XB95_2 | plasma | Baseline |
SA393588 | XB32_1 | plasma | Baseline |
SA393589 | XB44_1 | plasma | Baseline |
SA393590 | XB20_1 | plasma | Baseline |
SA393591 | XB24_1 | plasma | Baseline |
SA393592 | XB79_1 | plasma | Baseline |
SA393593 | XB1_1 | plasma | Baseline |
SA393594 | XB101_1 | plasma | Baseline |
SA393595 | XB70_3 | plasma | Baseline |
SA393596 | XB14_2 | plasma | Baseline |
SA393597 | XB95_1 | plasma | Baseline |
SA393598 | XB18_1 | plasma | Baseline |
SA393599 | XB100_2 | plasma | Baseline |
SA393600 | XB70_2 | plasma | Baseline |
SA393601 | XB70_1 | plasma | Baseline |
SA393602 | XB68_1 | plasma | Baseline |
SA393603 | XB2_1 | plasma | Baseline |
SA393604 | XB14_1 | plasma | Baseline |
SA393605 | XB100_1 | plasma | Baseline |
SA393606 | XB89_1 | plasma | Baseline |
SA393607 | XB68_2 | plasma | Baseline |
SA393608 | XB1_2 | plasma | Baseline |
SA393609 | XB100_3 | plasma | Baseline |
SA393610 | XB79_5 | plasma | Baseline |
SA393611 | XB38_4 | plasma | Baseline |
SA393612 | XB94_1 | plasma | Baseline |
SA393613 | XB20_3 | plasma | Baseline |
SA393614 | XB68_3 | plasma | Baseline |
SA393615 | XB34_1 | plasma | Baseline |
SA393616 | XB6_1 | plasma | Baseline |
SA393617 | XB107_2 | plasma | Baseline |
SA393618 | XB62_1 | plasma | Baseline |
SA393619 | XB21_2 | plasma | Baseline |
SA393620 | XB38_3 | plasma | Baseline |
SA393621 | XB33_3 | plasma | Baseline |
SA393622 | XB21_1 | plasma | Baseline |
Collection:
Collection ID: | CO003753 |
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: | TR003769 |
Treatment Summary: | Baseline sample no treatment. |
Human Fasting: | Yes |
Sample Preparation:
Sampleprep ID: | SP003767 |
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. Briefly, 1 mL of ice-cold MTBE and 260 μL methanol was added to 40 μL of the plasma spiked-in with 40 µL deuterated lipid internal standards (Sciex, cat# 5040156, lot# LPISTDKIT-103). The samples were then agitated at 4°C for 30 minutes. After the addition of 250 μL of ice-cold water, the samples were vortexed for 1 minute and centrifuged at 3,800 g for five minutes at 4°C. The upper organic phase contained the lipids, the lower aqueous phase contained the metabolites, and the proteins were precipitated at the bottom of the well. For quality control, three reference plasma samples (40 µL plasma) as well as one control sample lacking any sample were processed in parallel per plate. For lipidomics, 700 µL of the organic phase was dried down under a stream of nitrogen and resolubilized in 200 µL of methanol for storage at -20°C until analysis. On the day of the analysis, samples were dried down, resuspended in 300 µL of 10 mM ammonium acetate in 90:10 methanol:toluene and centrifuged at 3,800 g for five minutes at 4°C. |
Sampleprep Protocol Filename: | lipidomics_process.pdf |
Extract Storage: | -80℃ |
Combined analysis:
Analysis ID | AN005963 |
---|---|
Analysis type | MS |
Chromatography type | None (Direct infusion) |
Chromatography system | none |
Column | none |
MS Type | ESI |
MS instrument type | QTRAP |
MS instrument name | 5500 QTRAP MS System |
Ion Mode | UNSPECIFIED |
Units | nmol/g |
Chromatography:
Chromatography ID: | CH004531 |
Chromatography Summary: | Check the protocol for details |
Instrument Name: | none |
Column Name: | none |
Column Temperature: | NA |
Flow Gradient: | NA |
Flow Rate: | NA |
Internal Standard: | Yes |
Solvent A: | none |
Solvent B: | none |
Chromatography Type: | None (Direct infusion) |
MS:
MS ID: | MS005678 |
Analysis ID: | AN005963 |
Instrument Name: | 5500 QTRAP MS System |
Instrument Type: | QTRAP |
MS Type: | ESI |
MS Comments: | Complex lipids were quantified using a targeted MS-based approach using the Lipidyzer Platform. Lipid extracts were analyzed using the Lipidyzer platform that comprises a 5500 QTRAP system equipped with a SelexION differential mobility spectrometry (DMS) interface (Sciex) and a high flow LC-30AD solvent delivery unit (Shimazdu, Columbia, MD). Briefly, lipid molecular species were identified and quantified using multiple reaction monitoring (MRM) and positive/negative ionization switching. Two acquisition methods were employed covering 13 lipid classes; method 1 had SelexION voltages turned on while method 2 had SelexION voltages turned off. Data quality was ensured by i) tuning the DMS compensation voltages using a set of lipid standards (cat# 5040141, Sciex) after each cleaning, more than 24 hours of idling or three days of consecutive use, ii) performing a quick system suitability test (QSST) (cat# 5040407, Sciex) before each batch to ensure acceptable limit of detection for each lipid class, and iii) triplicate injection of lipids extracted from a reference plasma sample (cat# 4386703, Sciex) at the beginning of the batch. Lipidyzer data were reported by the Lipidomics Workflow Manager (LWM, v1.0.5.0) software which calculates concentrations for each detected lipid as the average intensity of the analyte MRM divided by the average intensity of the most structurally similar internal standard (IS) MRM multiplied by its concentration. Lipids detected in less than 2/3 of the samples were discarded and missing values were imputed by drawing from a random distribution of low values class-wise in the corresponding sample. Lipid abundances were reported as concentrations in nmol/g. |
Ion Mode: | UNSPECIFIED |
Analysis Protocol File: | lipidomics_process.pdf |