Summary of Study ST001681

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 PR001080. The data can be accessed directly via it's Project DOI: 10.21228/M83H5W 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 IDST001681
Study TitleIntegrated trajectories of the maternal metabolome, proteome, and immunome predict labor onset
Study SummaryEstimating the time of delivery is of high clinical importance as pre- and post-term deviations are associated with complications for the mother and her offspring. However, current estimation approaches are inaccurate. As pregnancy progresses towards labor, major transitions occur in fetomaternal immune, metabolic, and endocrine systems that culminate in the delivery of the fetus. The comprehensive characterization of metabolic, proteomic and immune cell events that precede the spontaneous onset of labor is a key step to understanding these physiological transitions and identifying predictive biomarkers of parturition. Here, over 7,000 circulating plasma analytes and peripheral immune cell responses collected during the last 100 days of pregnancy were integrated into a multi-omic model that accurately predicted the time to spontaneous onset of labor (R = 0.85, p-value = 1.2e-40, training set; R = 0.81, p-value = 3.9e-7, independent test set). Coordinated fluctuations marked a molecular shift from pregnancy progression to pre-labor onset biology 2–4 weeks before delivery. Our study lays the groundwork for developing blood-based methods for predicting the onset of labor, anchored in mechanisms shared in preterm, term, and postterm pregnancies.
Institute
Stanford University
Last NameContrepois
First NameKevin
Address1291 Welch rd, Biomedical innovations building-Room 4400, STANFORD, California, 94305, USA
Emailkcontrep@stanford.edu
Phone6506664538
Submit Date2021-02-02
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-07-22
Release Version1
Kevin Contrepois Kevin Contrepois
https://dx.doi.org/10.21228/M83H5W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001080
Project DOI:doi: 10.21228/M83H5W
Project Title:Untargeted plasma metabolomics to predict the time to spontaneous onset of labor
Project Summary:Longitudinal blood collection during the last 100 days of pregnancy and untargeted LC-MS metabolomics to predict the time to spontaneous onset of labor
Institute:Stanford University
Department:Genetics
Last Name:Contrepois
First Name:Kevin
Address:1291 Welch rd, Biomedical innovations building-Room 4400, STANFORD, California, 94305, USA
Email:kcontrep@stanford.edu
Phone:6507239914

Subject:

Subject ID:SU001758
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Timepoint
SA154663026_31_AG1
SA154664051_27_AG1
SA154665050_32_AG1
SA154666027_24_AG1
SA154667091_30_AG1
SA154668025_26_AG1
SA154669075_31_AG1
SA154670024_27_AG1
SA154671021_27_AG1
SA154672098_26_AG1
SA154673041_25_AG1
SA154674022_26_AG1
SA154675028_31_AG1
SA154676052_24_AG1
SA154677093_27_AG1
SA154678045_27_AG1
SA154679086_30_AG1
SA154680035_27_AG1
SA154681036_28_AG1
SA154682042_24_AG1
SA154683040_25_AG1
SA154684001_26_AG1
SA154685083_28_AG1
SA154686043_27_AG1
SA154687044_30_AG1
SA154688032_24_AG1
SA154689033_31_AG1
SA154690087_30_AG1
SA154691034_26_AG1
SA154692054_32_AG1
SA154693074_30_AG1
SA154694072_24_AG1
SA154695007_28_AG1
SA154696008_28_AG1
SA154697063_30_AG1
SA154698014_27_AG1
SA154699019_27_AG1
SA154700100_29_AG1
SA154701065_27_AG1
SA154702068_27_AG1
SA154703003_25_AG1
SA154704005_25_AG1
SA154705067_30_AG1
SA154706006_25_AG1
SA154707057_27_AG1
SA154708012_25_AG1
SA154709017_31_AG1
SA154710056_25_AG1
SA154711018_27_AG1
SA154712016_32_AG1
SA154713099_24_AG1
SA154714073_27_AG1
SA154715055_27_AG1
SA154716052_36_BG2
SA154717065_38_BG2
SA154718055_35_BG2
SA154719041_30_BG2
SA154720068_37_BG2
SA154721067_37_BG2
SA154722042_27_BG2
SA154723043_38_BG2
SA154724063_38_BG2
SA154725045_33_BG2
SA154726072_36_BG2
SA154727057_36_BG2
SA154728075_36_BG2
SA154729056_37_BG2
SA154730050_36_BG2
SA154731051_38_BG2
SA154732044_36_BG2
SA154733074_37_BG2
SA154734087_36_BG2
SA154735018_31_BG2
SA154736017_33_BG2
SA154737016_34_BG2
SA154738098_36_BG2
SA154739019_31_BG2
SA154740093_38_BG2
SA154741083_36_BG2
SA154742021_34_BG2
SA154743014_30_BG2
SA154744099_38_BG2
SA154745005_29_BG2
SA154746003_30_BG2
SA154747001_33_BG2
SA154748100_37_BG2
SA154749006_30_BG2
SA154750012_29_BG2
SA154751008_32_BG2
SA154752007_36_BG2
SA154753024_29_BG2
SA154754022_31_BG2
SA154755034_35_BG2
SA154756033_33_BG2
SA154757086_36_BG2
SA154758035_31_BG2
SA154759040_29_BG2
SA154760036_30_BG2
SA154761025_30_BG2
SA154762032_27_BG2
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Collection:

Collection ID:CO001751
Collection Summary:Healthy pregnant women receiving routine antepartum care were eligible for the study if they were within 18 to 50 years of age, body mass index (BMI) < 40 in their 2nd or 3rd trimester of pregnancy as determined by their clinician using LMP and ultrasound estimates of GA, and had no immune-modifying co-morbidities or medication usage. Participants were followed longitudinally until parturition, collecting 1-3 blood samples throughout the third trimester (n = 53 participants). Blood was collected into EDTA tubes, kept on ice, and centrifuged (1500 x g, 20 min) at 4°C within 60 min. Separated plasma was stored at –80°C until further processing.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001771
Treatment Summary:There was no treatment.

Sample Preparation:

Sampleprep ID:SP001764
Sampleprep Summary:Plasma samples were thawed on ice, prepared and analyzed randomly as previously described (Contrepois et al., 2015). Briefly, metabolites were extracted using 1:1:1 acetone:acetonitrile:methanol, evaporated to dryness under nitrogen and reconstituted in 1:1 methanol:water before analysis. Each sample was spiked-in with 15 analytical-grade internal standards (IS).

Combined analysis:

Analysis ID AN002742 AN002743 AN002744 AN002745
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) Agilent Zorbax SBaq (50 x 2.1mm,1.7um) Agilent Zorbax SBaq (50 x 2.1mm,1.7um)
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 MS Counts MS Counts MS Counts MS Counts

Chromatography:

Chromatography ID:CH002026
Chromatography Summary:HILIC experiments were performed using a ZIC-HILIC column 2.1x100 mm, 3.5μm, 200Å (Merck Millipore) 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).(Contrepois et al., 2015)
Instrument Name:Thermo Vanquish
Column Name:SeQuant ZIC-HILIC (100 x 2.1mm,3.5um)
Column Temperature:40
Flow Rate:0.5 ml/min
Solvent A:95% acetonitrile/5% water; 10 mM ammonium acetate
Solvent B:95% acetonitrile/5% water; 10 mM ammonium acetate
Chromatography Type:HILIC
  
Chromatography ID:CH002027
Chromatography Summary:RPLC experiments were performed using a Zorbax SBaq column 2.1 x 50 mm, 1.7 μm, 100Å (Agilent Technologies) and mobile phase solvents consisting of 0.06% acetic acid in water (A) and 0.06% acetic acid in methanol (B). (Contrepois et al., 2015)
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Agilent Zorbax SBaq (50 x 2.1mm,1.7um)
Column Temperature:60
Flow Rate:0.6 ml/min
Solvent A:100% water; 0.06% acetic acid
Solvent B:100% methanol; 0.06% acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002539
Analysis ID:AN002742
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data processing. Data from each mode were independently processed using Progenesis QI software (v2.3, Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and 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. Inter- and intra-batch variations were corrected using the LOESS (locally estimated scatterplot smoothing Local Regression) normalization method on QC injected repetitively along the batches (span = 0.75). Data were acquired in five and three batches for HILIC and RPLC modes, respectively. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and resulted in a dataset containing 3,529 metabolic features that was used for downstream analysis. Metabolic features of interest were tentatively identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:POSITIVE
Capillary Temperature:375C
Capillary Voltage:3.4kV
Collision Energy:25 & 35 NCE
Collision Gas:N2
Dry Gas Temp:310C
  
MS ID:MS002540
Analysis ID:AN002743
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data processing. Data from each mode were independently processed using Progenesis QI software (v2.3, Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and 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. Inter- and intra-batch variations were corrected using the LOESS (locally estimated scatterplot smoothing Local Regression) normalization method on QC injected repetitively along the batches (span = 0.75). Data were acquired in five and three batches for HILIC and RPLC modes, respectively. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and resulted in a dataset containing 3,529 metabolic features that was used for downstream analysis. Metabolic features of interest were tentatively identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:NEGATIVE
Capillary Temperature:375C
Capillary Voltage:3.4kV
Collision Energy:25 & 35 NCE
Collision Gas:N2
Dry Gas Temp:310C
  
MS ID:MS002541
Analysis ID:AN002744
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data processing. Data from each mode were independently processed using Progenesis QI software (v2.3, Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and 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. Inter- and intra-batch variations were corrected using the LOESS (locally estimated scatterplot smoothing Local Regression) normalization method on QC injected repetitively along the batches (span = 0.75). Data were acquired in five and three batches for HILIC and RPLC modes, respectively. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and resulted in a dataset containing 3,529 metabolic features that was used for downstream analysis. Metabolic features of interest were tentatively identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:POSITIVE
Capillary Temperature:375C
Capillary Voltage:3.4kV
Collision Energy:25 & 50 NCE
Collision Gas:N2
Dry Gas Temp:310C
  
MS ID:MS002542
Analysis ID:AN002745
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data processing. Data from each mode were independently processed using Progenesis QI software (v2.3, Nonlinear Dynamics, Durham, NC). Metabolic features from blanks and 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. Inter- and intra-batch variations were corrected using the LOESS (locally estimated scatterplot smoothing Local Regression) normalization method on QC injected repetitively along the batches (span = 0.75). Data were acquired in five and three batches for HILIC and RPLC modes, respectively. Missing values were imputed by drawing from a random distribution of low values in the corresponding sample. Data from each mode were merged and resulted in a dataset containing 3,529 metabolic features that was used for downstream analysis. Metabolic features of interest were tentatively identified by matching fragmentation spectra and retention time to analytical-grade standards when possible or matching experimental MS/MS to fragmentation spectra in publicly available databases.
Ion Mode:NEGATIVE
Capillary Temperature:375C
Capillary Voltage:3.4kV
Collision Energy:25 & 50 NCE
Collision Gas:N2
Dry Gas Temp:310C
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