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MB Sample ID: SA154685
| Local Sample ID: | 083_28_A |
| Subject ID: | SU001758 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001758 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 083_28_A | SA154685 | FL018234 | G1 | Timepoint |
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 |
