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MB Sample ID: SA220212
| Local Sample ID: | ID_44 |
| Subject ID: | SU002377 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002377 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| ID_44 | SA220212 | FL027454 | Severe | Group |
Collection:
| Collection ID: | CO002370 |
| Collection Summary: | Individuals with COVID-19 were admitted to the Hospital das Clínicas and Hospital das Clínicas de Campanha or recruited at the Laboratório Profª Margarida Dobler Komma at the Federal University of Goiás, Goiânia, Brazil between June 2020 to February 2021, before vaccination rollout. Blood samples were collected in EDTA tubes from 150 individuals who had confirmed SARS-CoV-2 infection by RT-qPCR test from nasopharyngeal swabs or by serological assays to detect specific IgM/IgG antibodies (Eco diagnostics); and control donors (n=27), who were negative for SARS-CoV-2 infection confirmed by RT-qPCR from nasopharyngeal swabs and serological IgM/IgG tests. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR002389 |
| Treatment Summary: | The criteria defined on COVID-19 Treatment Guidelines (National Institute of Health, USA) and World Health Organization [21,22] were used to stratify individuals with COVID-19 into mild disease (individuals presenting various signs and symptoms without shortness of breath, dyspnea, or abnormal chest imaging), moderate disease (individuals presenting radiologically confirmed pneumonitis, hospitalization and oxygen therapy), severe disease (dyspnea, respiratory frequency ≥30 breaths/min, saturation of oxygen [SpO2] ≤ 93%, and/or lung infiltrates >50% within 24 to 48 hours, including individuals that required monitoring and treatment in Intensive Care Unit and mechanical ventilation), or fatal COVID-19. |
Sample Preparation:
| Sampleprep ID: | SP002383 |
| Sampleprep Summary: | For metabolomics analyses, cold acetonitrile was added to plasma samples (2:1, v/v) vortexed and centrifuged (10 min, 10000 rpm at 4 °C) for protein precipitation. Stable isotopes caffeine-¹³C3, tyrosine-15N and progesterone-d9 were used as internal standards. |
Combined analysis:
| Analysis ID | AN003743 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1220 Infinity |
| Column | Agilent Zorbax Eclipse Plus C18 (150 x 4.6mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH002773 |
| Chromatography Summary: | The binary mobile phases were water 0.5% formic acid with 5 mM of ammonium formate (A), and acetonitrile (B). Their gradient elution started with 20% (B) for 5 min, then linearly increased to 100% (B) in 30 min and kept constant for 8 min in 100% (B). The eluent was restored to the initial conditions in 4 minutes to re-equilibrate the column and held for the remaining 8 minutes. The flow rate was kept at 0.5 mL min-1. The injection volume for analysis was 3 μL, and the column temperature was set at 35 °C. |
| Instrument Name: | Agilent 1220 Infinity |
| Column Name: | Agilent Zorbax Eclipse Plus C18 (150 x 4.6mm,3.5um) |
| Column Temperature: | 35 |
| Flow Gradient: | gradient elution started with 20% (B) for 5 min, then linearly increased to 100% (B) in 30 min and kept constant for 8 min in 100% (B). The eluent was restored to the initial conditions in 4 minutes to re-equilibrate the column and held for the remaining 8 minutes. |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% water; 0.5% formic acid; 5 mM of ammonium formate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003490 |
| Analysis ID: | AN003743 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The electrospray ionization was operating with the following settings: spray voltage 3.5 kV; capillary temperature: 269 °C; S-lens RF level 50 V; sheath gas flow rate at 53 L min-1; aux gas flow rate at 14 L min-1; sweep gas flow rate 3 L min-1. The high-resolution mass-spectrometry was obtained under full MS/dd-MS2 mode. The mass range in the full MS scanning experiments was m/z 80-1200. The max IT was set at 200 ms, and AGC target was set at 1 x 106. For fragmentation acquisition, the top 5 (TopN, 5, loop count 5) most abundant precursors were sequentially transferred into the C-Trap (AGC target 1 x 105; max IT 50 ms) for collision. The collision energy for target analytes was 20, 30 and 35 eV. Resolving power was set at 140,000 and 70,000 for full MS and dd-MS2 acquisitions, respectively. Proteowizard software was used to convert .raw files into mzXML format and apLCMS software was used to perform peak deconvolution and detection, to filter noise, to align mass-to-charge ratio (m/z) and retention time and to quantify metabolite features, which are defined by a specific m/z, retention time and intensity values for each sample. |
| Ion Mode: | POSITIVE |
