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MB Sample ID: SA210384
| Local Sample ID: | CNMI_54 |
| Subject ID: | SU002280 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002280 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CNMI_54 | SA210384 | FL025693 | Severe | Label |
| CNMI_54 | SA210384 | FL025693 | 0 | Gender |
| CNMI_54 | SA210384 | FL025693 | 0 | HTA |
| CNMI_54 | SA210384 | FL025693 | 0 | Obesity |
| CNMI_54 | SA210384 | FL025693 | 1 | Dyspnoea |
Collection:
| Collection ID: | CO002273 |
| Collection Summary: | Samples were collected at hospital admission or within the first days after hospitalization (median = 2 days) and before treatment with immunotherapy against IL-6 (e.g., tocilizumab), interferon beta, corticoids, or ribavirin, among others. Plasma samples were obtained after centrifugation blood in EDTA tubes and stored at -80 °C. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002292 |
| Treatment Summary: | Plasma samples were inactivated with cold (-20°C) MeOH : EtOH (1:1, v/v) and vortex-mixed for 1 min, incubated on ice for 5 min, and centrifuged for 20 min at 16000 xg at 4°C. The resulting supernatant was stored at -80°C until analysis. Due to the broad differences in physical-chemical properties of metabolites, we used GC-MS (focused on small molecules that can be made volatile by derivatization) and CE-MS (focused on polar and ionic compounds) in order to increase the metabolite coverage. Sample preparation for GC-MS and CE-MS was detailed in the uploaded file in sample preparation part. |
| Treatment Protocol Filename: | Sample_treatment.pdf |
Sample Preparation:
| Sampleprep ID: | SP002286 |
| Sampleprep Summary: | For GC-MS analysis samples, 200 µL of frozen plasma supernatant was thawed at room temperature and 30 µL of 80 mg/L deuterated palmitic acid in MeOH was added as internal standard (IS). After samples were evaporated to dryness a two-step derivatization process was done. For CE-MS analysis, 200 µL of frozen supernatant was thawed until room temperature and it was evaporated to dryness using a SpeedVac Concentrator System (Thermo Fisher Scientific, MA). Afterwards, 100 µL of 0.2 mM methionine sulfone (MetS) as internal standard (IS) in 0.1 M formic acid solution was added. Samples were vortex mixed, filtered and subsequently centrifuged. More detailed information is included in the attached pdf. |
Combined analysis:
| Analysis ID | AN003591 | AN003592 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | CE | GC |
| Chromatography system | Agilent 7100 CE | 8890 |
| Column | silica capillary (100 cm; inner diameter,50um,Agilent Technologies) | Agilent DB5-MS (30m x 0.25mm, 0.25um) |
| MS Type | ESI | EI |
| MS instrument type | TOF | Single quadrupole |
| MS instrument name | Agilent CE-TOFMS | Agilent 5977B |
| Ion Mode | POSITIVE | UNSPECIFIED |
| Units | Peak Area | Corrected areas |
Chromatography:
| Chromatography ID: | CH002653 |
| Chromatography Summary: | Metabolite separation was performed in a fused silica capillary (100 cm; inner diameter, 50 µm, Agilent Technologies). Before each analysis, background electrolyte (BFE) (0.8 M formic acid solution in 10 % MeOH; v/v) was flushed for 5 min (950 mbar). Samples injections were performed over 50 s at 50 mbar and BGE was injected after each injection for 10 s at 100 mbar to improve reproducibility. The separation was carried out with an internal pressure of 25 mbar and 30 kV voltage with a total analytical run time of 35 min. |
| Methods Filename: | Sample_Analysis.pdf |
| Instrument Name: | Agilent 7100 CE |
| Column Name: | silica capillary (100 cm; inner diameter,50um,Agilent Technologies) |
| Chromatography Type: | CE |
| Chromatography ID: | CH002654 |
| Chromatography Summary: | The flow rate of helium carrier gas was constant at 1.1359 mL/min and the injector temperature was set at 250 °C. The lock of the retention time (RTL) relative to the internal standard (methyl stearate) peak at 19.66 min was performed. The oven temperature gradient was initially set at 60 °C and was maintained for 1 min. Then it was raised by 10 °C/min until it reached 325 °C, and then was held at this temperature for 10 min before cooling down. The total analysis run time was 37.5 min. |
| Methods Filename: | Sample_Analysis.pdf |
| Instrument Name: | 8890 |
| Column Name: | Agilent DB5-MS (30m x 0.25mm, 0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS003346 |
| Analysis ID: | AN003591 |
| Instrument Name: | Agilent CE-TOFMS |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | Data were acquired in positive ionization polarity with a full scan range from 70 to 1000 m/z at a rate of 1.36 scan/s. The rest of MS conditions were: fragmentor set to 125 V, skimmer to 65 V, OCT RF Vpp to 750 V, drying gas temperature to 200 °C, flow rate to 10 L/min, nebulizer to 10 psig, and capillary voltage to 3500 V. The sheath liquid used for detection contained two reference masses (5 µL of purine with m/z 121.0509 and 5 µL of HP-0921 with m/z 922.0098) in MeOH/water (1/1; v/v) with 1 mM formic acid and the flow rate was set to 0.6 mL/min (split 1:100). The data acquisition was made using the Agilent MassHunter Workstation (Agilent Technologies). |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Sample_Analysis.pdf |
| MS ID: | MS003347 |
| Analysis ID: | AN003592 |
| Instrument Name: | Agilent 5977B |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | The transfer line temperature was stablished at 280 °C and the electron ionization (EI) source was operated at 70 eV and the filament source temperature was set at 200 °C. Mass spectra were collected over a mass range of 50 - 600 m/z at a scan rate of 2.7 scans/s. Data were acquired using the Agilent MassHunter Workstation GC/MS Data Acquisition (version 10.0). |
| Ion Mode: | UNSPECIFIED |
| Analysis Protocol File: | Sample_Analysis.pdf |
