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MB Sample ID: SA226504
Local Sample ID: | Plasma69-02_75_1_2427 |
Subject ID: | SU002387 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002387 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Plasma69-02_75_1_2427 | SA226504 | FL027491 | Severe | Severity of Disease |
Collection:
Collection ID: | CO002380 |
Collection Summary: | In this retrospective cohort study, blood samples were collected from donors who tested positive for COVID-19 and presented with no, mild or severe symptoms between March 20 until July 17, 2020. Patients were diagnosed with COVID-19 using a nasal swab PCR test and later divided into three groups (asymptomatic, mild, and severe) based on their clinical presentation. Each donor gave a 10 ml blood sample, one half of which was collected in a plain tube and the other half in an EDTA vacutainer. A total of 85 samples were collected (30 COVID-19-positive asymptomatic, 10 COVID-19-positive with mild symptoms, and 45 COVID-19-positive with severe symptoms) for the purpose of this study. COVID-19-positive asymptomatic individuals were identified as a result of the national screening campaigns. Symptomatic COVID-19 patients were classified into mild or severe based on guidelines published by Abu Dhabi Department of Health (circular number 33, 19th April 2020). Patients with mild disease presented with upper respiratory tract infection and symptoms like fever, dry cough, sore throat, runny nose, muscle and joint pains without shortness of breath. Patients with severe disease presented with severe pneumonia and symptoms like fever, cough, dyspnea and fast breathing (>30 per minute), in addition to oxygen saturation <90%. Immediately upon sample collection, the hospital laboratory staff separated and tested the serum for CRP, D-dimer, ferritin, IL-6 and LDH; a complete blood count was also performed on each sample. Whole blood samples were also aliquoted and frozen at −80 0C for subsequent processing and analysis. The study was jointly approved by the Ministry of Health, Abu Dhabi and Dubai Health Authority (DOH/CVDC/2020/1949) on the understanding that samples will be number-coded to hide patient identity, that no personal information will be shared with a third party and that no sample analysis can be performed by entities other than the Research Institute of Medical and Health Sciences (RIMHS), the University of Sharjah (UOS) without prior written approval. |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR002399 |
Treatment Summary: | No treatment, study examines the predictive ability of metabolomic profiling models to predict covid disease severity |
Sample Preparation:
Sampleprep ID: | SP002393 |
Sampleprep Summary: | Plasma was obtained after the collection of samples into heparinized tubes followed by centrifugation for 5 minutes (3000g). The samples were stored at –80 ºC for long-term storage until further metabolomics analysis. An aliquot of plasma sample into a microcentrifuge tube and add cold methanol into the sample at 3:1 v/v (i.e., 30 μL sample, add 90 μL cold methanol) vortex and allow to sit in –20ºC for two hrs. Next, centrifuge the samples at 20,817 x g for 15 min at 4ºC. Then, transfer the supernatant to a new microcentrifuge tube. Usually, transfer three times the original sample volume (i.e., for 30 μL sample, add 90 μL cold methanol, then transfer 90 μL supernatant). Dry down the sample using Speed vac at 30 – 40°C. Store the dried sample in a –80ºC freezer for further use or dissolve it in solvent for LC-MS/MS analysis |
Combined analysis:
Analysis ID | AN003757 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Bruker Elute |
Column | Hamilton Intensity Solo 2 C18 |
MS Type | ESI |
MS instrument type | QTOF |
MS instrument name | Bruker timsTOF |
Ion Mode | POSITIVE |
Units | AU |
Chromatography:
Chromatography ID: | CH002780 |
Instrument Name: | Bruker Elute |
Column Name: | Hamilton Intensity Solo 2 C18 |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003500 |
Analysis ID: | AN003757 |
Instrument Name: | Bruker timsTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
MS Comments: | The ESI source with dry nitrogen gas was 10 L/min, and the drying temperature was equal to 220℃ with nebulizer gas pressure set to 2.2 bar. The capillary voltage of the ESI was 4500 V and the Plate Offset 500 V. MS acquisition scan was set at 20-1300 m/z and the collision energy at 7 eV. Sodium formate was injected as an external calibrant between 0.1 and 0.3 minutes. A total volume of 10 µL sample was injected into the TIMS-TOF MS. |
Ion Mode: | POSITIVE |