Summary of Study ST002937
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 PR001827. The data can be accessed directly via it's Project DOI: 10.21228/M8JQ6C 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 | ST002937 |
| Study Title | Deep Metabolic Phenotyping of Newborn Cord Blood Reveals Maternal-Fetal Interactions and Disease Risk |
| Study Type | Untargeted MS and Targeted MS |
| Study Summary | Metabolites are small molecules circulating in the mother, placental, and fetal blood that can have a profound effect on a developing fetus (1, 2). Many metabolites from pregnant mothers cross the placenta to provide energy, structural components, essential nutrients, and signals to the developing fetus (3, 4). Issues with proper transmission of metabolites to the fetus, whether through gestational diabetes, placental insufficiency, or other sources can permanently damage the fetus (5-7). However, quantification of many metabolites entering and exiting the fetus are unknown; associations between microbial metabolites in umbilical cords and disease have not been thoroughly investigated; and there remains a lack of quantifiable metabolic effects of some of the most common medications administered during pregnancy and parturition. Here we identified and quantified many metabolites with a gradient between arterial and venous cord blood; we demonstrated that exogenous metabolites in umbilical cords associate with many health outcomes; and we show that medications can profoundly alter the metabolic milieu of the fetus. We greatly expanded the number of metabolites that demonstrate a gradient between arterial and venous blood, indicating absorption by the fetus, including several essential fatty acids. The microbial metabolites 3-indolepropionic acid, hydroxyhippuric acid and others are associated with many newborn diseases. Lastly, we show that exogenous medications like bupivacaine and betamethasone can have a profound impact on newborn metabolic profile. This study is the most comprehensive study of umbilical cord metabolic and disease associations to date. It reveals important aspects of fetal biology, like the reliance on specific essential fatty acid and taurine. It suggests several interventions in pregnant mothers that may help newborn health, including new fatty acids. This study serves as a valuable reference for investigators wishing to better understand the impact of medications on the developing fetus and neonate. |
| Institute | Stanford University |
| Department | Department of Genetics |
| Laboratory | Snyder Lab |
| Last Name | Lancaster |
| First Name | Samuel |
| Address | 240 Pasteur Dr, BMI bldg 4400, Stanford California, 94305 |
| slancast@stanford.edu | |
| Phone | (612)-600-4033 |
| Submit Date | 2023-08-31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004817 | AN004818 | AN004819 | AN004820 | AN004821 | AN004822 |
|---|---|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | HILIC | None (Direct infusion) | None (Direct infusion) |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Vanquish | Thermo Vanquish | Shimazdu LC-30AD | Shimazdu LC-30AD |
| Column | Agilent Zorbax SBaq (50 x 2.1mm x 1.7 um) | Agilent Zorbax SBaq (50 x 2.1mm x 1.7 um) | Merck SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) | Merck SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) | None | None |
| MS Type | ESI | ESI | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap | QTRAP | QTRAP |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap | ABI Sciex 5500 QTrap | ABI Sciex 5500 QTrap |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Relative Abundance | Relative Abundance | Relative Abundance | Relative Abundance | Relative Abundance | Relative Abundance |
MS:
| MS ID: | MS004563 |
| Analysis ID: | AN004817 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | 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 SERRF. Data quality post-normalization was verified by ensuring clustering of pooled sample replicates on a principal component analysis (PCA) plot. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004564 |
| Analysis ID: | AN004818 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | 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 SERRF. Data quality post-normalization was verified by ensuring clustering of pooled sample replicates on a principal component analysis (PCA) plot. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004565 |
| Analysis ID: | AN004819 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | 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 SERRF. Data quality post-normalization was verified by ensuring clustering of pooled sample replicates on a principal component analysis (PCA) plot. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004566 |
| Analysis ID: | AN004820 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | 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 SERRF. Data quality post-normalization was verified by ensuring clustering of pooled sample replicates on a principal component analysis (PCA) plot. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004567 |
| Analysis ID: | AN004821 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | Lipidyzer data were reported by the Lipidomics Workflow Manager (LWM, v1.0.5.0) software which calculates concentrations for each detected lipid as average intensity of the analyte MRM relative to 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. Data quality was verified by ensuring clustering of the quality control replicates analyzed on a PCA plot. We detected lipid species belonging to 13 classes (e.g. CE, CER, DAG, FFA, HCER, LCER, DCER, LPE, LPC, PC, PE, SM, TAG) and their abundance were reported as concentrations in nmol/g. The Q1 and Q3 mass provided in the metadata were used to target specific lipid classes. Lipids with the designated Q1 mass, also known as the parent ion, are selected from the first quadrupole. The lipids are then fragmented and sent to the third quadrupole. In the third quadrupole, the desired lipid class is selected based on its Q3 mass. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004568 |
| Analysis ID: | AN004822 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | QTRAP |
| MS Type: | ESI |
| MS Comments: | Lipidyzer data were reported by the Lipidomics Workflow Manager (LWM, v1.0.5.0) software which calculates concentrations for each detected lipid as average intensity of the analyte MRM relative to 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. Data quality was verified by ensuring clustering of the quality control replicates analyzed on a PCA plot. We detected lipid species belonging to 13 classes (e.g. CE, CER, DAG, FFA, HCER, LCER, DCER, LPE, LPC, PC, PE, SM, TAG) and their abundance were reported as concentrations in nmol/g. The Q1 and Q3 mass provided in the metadata were used to target specific lipid classes. Lipids with the designated Q1 mass, also known as the parent ion, are selected from the first quadrupole. The lipids are then fragmented and sent to the third quadrupole. In the third quadrupole, the desired lipid class is selected based on its Q3 mass. |
| Ion Mode: | NEGATIVE |
