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MB Sample ID: SA188765
| Local Sample ID: | Pat_87_NEG |
| Subject ID: | SU002097 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002097 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Pat_87_NEG | SA188765 | FL023212 | COVID_non-acute | group |
Collection:
| Collection ID: | CO002090 |
| Collection Summary: | Blood samples were collected in EDTA tubes from 84 adult patients who tested positive by PCR for SARS-CoV2 at the University of Virginia hospital between April and June 2020. Plasma prepared from the blood was stored at -70oC. A total of 48 of the samples were from out-patients and categorized as non-severe COVID-19, while 36 samples were categorized as severe COVID-19 based on the need for hospitalization and in some cases ICU and ventilator requirements (four and 25, respectively) |
| Sample Type: | Blood (plasma) |
| Collection Method: | EDTA Tubes |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR002109 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP002103 |
| Sampleprep Summary: | plasma samples were thawed on ice and 50 µL of plasma was retained for the metabolome analysis. Approximately 200 µL of cold methanol was added to the plasma sample and shaken vigorously to inactivate any potential viruses. The samples were stored in -80 ºC immediately until extraction for metabolomics experiments. For extraction, 200 µL of cold methanol was added to each tube, vortexed and shaken vigorously for 30 min at 4 ºC in a temperature controlled thermal shaker. Further 200 µL of chloroform and 400 µL of water were added, shaken vigorously and the top aqueous phase was recovered as a metabolite mixture of diverse chemical nature. Each metabolite extract was dried overnight in speedVac and reconstituted in 60 µL of 0.1% formic acid in water. Ten microliters from each tube were removed to create a pooled QC sample that was injected at the beginning and end of the MS sequence run and additional QC samples were injected after every 10 sample injections. |
| Processing Storage Conditions: | Described in summary |
| Extraction Method: | Described above |
| Extract Storage: | Described in summary |
| Sample Resuspension: | 0.1% formic acid |
Combined analysis:
| Analysis ID | AN003284 | AN003285 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C18 (100 x 2.1mm,2.6um) | Thermo Accucore C18 (100 x 2.1mm,2.6um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X tribrid | Thermo Orbitrap ID-X tribrid |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | intensity | intensity |
Chromatography:
| Chromatography ID: | CH002425 |
| Chromatography Summary: | Samples were injected in randomized fashion via a Thermo Vanquish UHPLC and separation of the polar metabolites was achieved using Thermo Accucore C18 column (Thermo Scientific; 2.1 x 100 mm; 1.5 µm) maintained at 30 °C. The injection volume was 10 µL. For the 15-minute gradient, the standard mobile phase for RPLC was A = 0.1% formic acid in water and B = 0.1% formic acid in methanol. The linear elution gradient was as follows: 0-8.0 minutes at 50% B, 8.0 – 13.0 minutes held at 98% B, 13.1 to 15.0 minutes revert to 0% B to re-equilibration for next injection at a flow rate of 0.25 mL/min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C18 (100 x 2.1mm,2.6um) |
| Column Temperature: | 30C |
| Flow Gradient: | 0-8 minutes 50% B, 8 - 13 minutes held at 98% B, 13.1 to 15.0 minutes revert to 0% B to re-equilibration for next injection |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003055 |
| Analysis ID: | AN003284 |
| Instrument Name: | Thermo Orbitrap ID-X tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | HESI) source was operated at 3.5 kV and 2.5kV for positive and negative modes, respectively. Ion source sheath gas was set at 35 and auxiliary gas at 7. Ion transfer tube temperature was maintained at 275 °C while vaporizer temperature was maintained at 320 °C. The instrument was set to acquire over the m/z range 67-1000, in full MS mode (1 µscan) at a resolution of 60,000 at a normalized AGC Target of 25% and 50 milliseconds of maximum injection time was allowed. RF lens amplitude was set at 35%. Tandem MS/MS performed by applying quadrupole isolation with an isolation window of 1.6 m/z. Activation type was set at HCD and masses were fragmented with HCD Assisted Collision Energy (%) of 15,35,50. Fragment masses were detected by Orbitrap at a resolution of 15,000. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003056 |
| Analysis ID: | AN003285 |
| Instrument Name: | Thermo Orbitrap ID-X tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | HESI) source was operated at 3.5 kV and 2.5kV for positive and negative modes, respectively. Ion source sheath gas was set at 35 and auxiliary gas at 7. Ion transfer tube temperature was maintained at 275 °C while vaporizer temperature was maintained at 320 °C. The instrument was set to acquire over the m/z range 67-1000, in full MS mode (1 µscan) at a resolution of 60,000 at a normalized AGC Target of 25% and 50 milliseconds of maximum injection time was allowed. RF lens amplitude was set at 35%. Tandem MS/MS performed by applying quadrupole isolation with an isolation window of 1.6 m/z. Activation type was set at HCD and masses were fragmented with HCD Assisted Collision Energy (%) of 15,35,50. Fragment masses were detected by Orbitrap at a resolution of 15,000. |
| Ion Mode: | NEGATIVE |
