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MB Sample ID: SA318884
Local Sample ID: | CB237-V |
Subject ID: | SU003050 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU003050 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
CB237-V | SA318884 | FL037889 | NA | type |
Collection:
Collection ID: | CO003043 |
Collection Summary: | Plasma was collected from umbilical cords at the Lucile Packard Children’s Hospital Stanford with permission from the Institutional Review Board (IRB #46411). All umbilical cords were collected and sent for clinically-indicated testing to Pathology where blood gas analysis was performed following Stanford protocol. Leftover and discarded samples were obtained for research. Arterial and venous blood were extracted from umbilical cords by heparinized syringe and transferred to low binding tubes. |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR003059 |
Treatment Summary: | Samples were centrifuged at 1300g for 10 minutes. Plasma was aliquoted in cryovials and frozen at -80°C. |
Sample Preparation:
Sampleprep ID: | SP003056 |
Sampleprep Summary: | Metabolites and lipids were extracted in 96-well high throughput fashion using a liquid-liquid biphasic separation with cold methyl tert-butyl ether (MTBE), methanol, and water. To begin, 1 mL MTBE was added to 40 μl of plasma and spiked with 40 μl of deuterated lipid internal standards (Sciex, cat# 5040156, lot# LPISTDKIT-103). The samples were agitated at 4°C for 30 minutes. After the addition of 250 μl cold water, samples were vortexed for 1 minute then centrifuged at 3,800 g for 5 minutes at 4°C. The upper organic phase contained the lipids while the lower aqueous phase contained metabolites with precipitated proteins at the bottom of the tube. For quality control, reference plasma samples (40 μl plasma), as well as controls lacking samples (blanks), were processed in parallel. 1) Metabolites: To further precipitate proteins, 500 μl 1:1:1 acetone: acetonitrile: methanol spiked with 16 labeled metabolite internal standards was added to 300 μl of the aqueous phase and 200 μl of the organic phase and incubated overnight at -20°C. After centrifugation at 3,800 g for 10 min at 4°C, the metabolic extracts were dried down under a stream of nitrogen gas and resuspended in 100 μl 50/50 methanol/water for LC-MS. 2) Complex lipids: 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. 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 5 min at 4°C. |
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 | Triple quadrupole | Triple quadrupole |
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 |
Chromatography:
Chromatography ID: | CH003640 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Agilent Zorbax SBaq (50 x 2.1mm x 1.7 um) |
Column Temperature: | 60 |
Flow Gradient: | N/A |
Flow Rate: | 0.6 ml/min |
Solvent A: | 0.06% acetic acid in water |
Solvent B: | 0.06% acetic acid in methanol |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH003641 |
Instrument Name: | Thermo Vanquish |
Column Name: | Merck SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
Column Temperature: | 40 |
Flow Gradient: | N/A |
Flow Rate: | 0.5 ml/min |
Solvent A: | 10 mM ammonium acetate in 50/50 acetonitrile/water |
Solvent B: | 10 mM ammonium acetate in 95/5 acetonitrile/water |
Chromatography Type: | HILIC |
Chromatography ID: | CH003642 |
Instrument Name: | Shimazdu LC-30AD |
Column Name: | None |
Column Temperature: | 20 |
Flow Gradient: | N/A |
Flow Rate: | 0.15 ml/min |
Solvent A: | 9:1 Methanol Toluene with 10 mM ammonium acetate |
Solvent B: | N/A |
Chromatography Type: | None (Direct infusion) |
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: | Triple quadrupole |
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: | Triple quadrupole |
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 |