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MB Sample ID: SA172005
| Local Sample ID: | B1_WU350-013_d0 |
| Subject ID: | SU001926 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001926 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| B1_WU350-013_d0 | SA172005 | FL020671 | 1 | batch |
| B1_WU350-013_d0 | SA172005 | FL020671 | d0 | WU day of presentation |
| B1_WU350-013_d0 | SA172005 | FL020671 | Yes | SARS-CoV-2 Positive |
| B1_WU350-013_d0 | SA172005 | FL020671 | Yes | Admitted to the ICU |
| B1_WU350-013_d0 | SA172005 | FL020671 | - | REMDESIVIR on |
| B1_WU350-013_d0 | SA172005 | FL020671 | - | DEXAMETHOSONE on |
Collection:
| Collection ID: | CO001919 |
| Collection Summary: | Over the period of March to August of 2020, blood specimens of 341 individuals who presented at Barnes Jewish Hospital or Christian Hospital located in Saint Louis, Missouri, USA were collected. Inclusion criteria were a physician-ordered SARS-CoV-2 nasopharyngeal swab polymerase chain reaction (PCR) test with a positive or negative outcome, availability of gender and age information, and an age greater than 18. Informed consent was obtained from all study participants. The clinical cohort consisted of 155 female and 186 184 male participants. Out of the 341 339 patients, 274 272 were considered SARS-CoV-2 positive (COV+) and 67 were considered SARS-CoV-2 negative (COV-). Two individuals included in the COV+ group were later determined to be infected with other coronaviruses (NL63, HKu1). Samples were collected at the time of enrollment (d0) to the study, and 3, 7, 14, 28, or 84 days post study entry. Clinically relevant medical information (e.g., patient-reported symptoms, date of symptom-onset, age, race, and BMI) was collected at the time of enrollment from the subject or the medical record. Participant plasma was stored at -80°C upon collection. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR001938 |
| Treatment Summary: | This observational study did not evaluate or apply any treatments or therapeutics. |
Sample Preparation:
| Sampleprep ID: | SP001932 |
| Sampleprep Summary: | Participant plasma, which had been stored at -80°C upon collection, was thawed on ice. A 50 µL aliquot was transferred onto the solid-phase-extraction (SPE)-system CAPTIVA-EMR Lipid 96-wellplate (Agilent Technologies) before addition of 250 µL of acetonitrile containing 1% formic acid (v/v) and 10 µM internal standard (consisting of uniformly 13C and 15N labeled amino acids from Cambridge Isotope Laboratories, Inc). The samples were mixed for 1 min at 360 rpm on an orbital shaker at room temperature prior to a 10 min incubation period at 4°C. Afterwards, 200 µL 80% acetonitrile in water (v/v) were added to the samples. The samples were mixed on an orbital shaker (360 rpm) for an additional 10 min at room temperature. The samples were then eluted into a 96-deepwell collection plate by centrifugation (10 min, 57 x g, 4°C followed by 2 min, 1000 x g, 4°C). Polar eluates were stored at -80°C until the day of LC/MS analysis. The SPE-plates were then washed twice with 500 µL 80% acetonitrile in water (v/v). Lipids still bound to the SPE-material were then released into a second elution plate, in two elution steps applying 2x 500 µL 1:1 methyl tert-butyl ether:methanol (v/v) onto the SPE cartridge and centrifuging for 2 min at 1000 g and 4°C. The combined eluates were dried under a stream of nitrogen (Biotage SPE Dry Evaporation System) at room temperature and reconstituted with 100 µL 1:1 2-propanol:methanol (v/v) prior to LC/MS analysis. |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | Described in summary |
Combined analysis:
| Analysis ID | AN002993 | AN002994 | AN002995 | AN002996 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | SeQuant ZIC-pHILIC (100 x 2.1mm,5um) | SeQuant ZIC-pHILIC (100 x 2.1mm,5um) | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF | QTOF |
| MS instrument name | Agilent 6540 QTOF | Agilent 6540 QTOF | Agilent 6545 QTOF | Agilent 6545 QTOF |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | Relative Intensity | Relative Intensity | Relative Intensity | Relative Intensity |
Chromatography:
| Chromatography ID: | CH002220 |
| Chromatography Summary: | An aliquot of 2 µL of polar metabolite extract was subjected to LC/MS analysis by using an Agilent 1290 Infinity II liquid-chromatography (LC) system coupled to an Agilent 6540 Quadrupole-Time-of-Flight (Q-TOF) mass spectrometer with a dual Agilent Jet Stream electrospray ionization source. Polar metabolites were separated on a SeQuant® ZIC®-pHILIC column (100 x 2.1 mm, 5 µm, polymer, Merck-Millipore) including a ZIC®-pHILIC guard column (2.1 mm x 20 mm, 5 µm). The column compartment temperature was maintained at 40°C and the flow rate was set to 250 µL/min. The mobile phases consisted of A: 95% water, 5% acetonitrile, 20 mM ammonium bicarbonate, 0.1% ammonium hydroxide solution (25% ammonia in water), 2.5 µM medronic acid, and B: 95% acetonitrile, 5% water, 2.5 µM medronic acid. The following linear gradient was applied: 0 to 1 min, 90% B; 12 min, 35% B; 12.5 to 14.5 min, 25% B; 15 min, 90% B followed by a re-equilibration phase of 4 min at 400µL/min and 2 min at 250µL/min. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | SeQuant ZIC-pHILIC (100 x 2.1mm,5um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0 to 1 min, 90% B; 12 min, 35% B; 12.5 to 14.5 min, 25% B; 15 min, 90% B followed by a re-equilibration phase of 4 min |
| Flow Rate: | 250ul/min |
| Solvent A: | 95% water/5% acetonitrile; 20 mM ammonium bicarbonate; 0.1% ammonium hydroxide; 2.5 µM medronic acid |
| Solvent B: | 95% acetonitrile/5% water; 2.5 µM medronic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002221 |
| Chromatography Summary: | An aliquot of 2 µL of lipid extract was subjected to LC/MS analysis by using an Agilent 1290 Infinity II LC-system coupled to an Agilent 6545 Q-TOF mass spectrometer with a dual Agilent Jet Stream electrospray ionization source. Lipids were separated on an Acquity UPLC® HSS T3 column (2.1 x 150 mm, 1.8 µm) including an Acquity UPLC® HSS T3 VanGuard Pre-Column (2.1 x 5mm, 1.8 µm) at a temperature of 60°C and a flow rate of 250 µL/min. The mobile phases consisted of A: 60% acetonitrile, 40% water, 0.1% formic acid, 10 mM ammonium formate, 2.5 µM medronic acid, and B: 90% 2-propanol, 10% acetonitrile, 0.1% formic acid, 10 mM ammonium formate (dissolved in 1 mL water). The following linear gradient was used: 0-2 min, 30% B; 17 min, 75% B; 20 min, 85%; 23-26 min, 100% B; 26, 30% B followed by a re-equilibration phase of 5 min. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| Column Temperature: | 60 |
| Flow Gradient: | The following linear gradient was used: 0-2 min, 30% B; 17 min, 75% B; 20 min, 85%; 23-26 min, 100% B; 26, 30% B followed by a re-equilibration phase of 5 min. |
| Flow Rate: | 0.25ml/min |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10mM ammonium formate; 2.5uM medronic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002782 |
| Analysis ID: | AN002993 |
| Instrument Name: | Agilent 6540 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | gas temperature 200°C, drying gas flow 10 L/min, nebulizer pressure 44 psi, sheath gas temperature 300°C, sheath gas flow 12 L/min, VCap 3000 V, nozzle voltage 2000 V, Fragmentor 100 V, Skimmer 65 V, Oct 1 RF Vpp 750 V, and m/z range 50-1700. Data were acquired under continuous reference mass correction at m/z 121.0509 and 922.0890 for positive ion mode and m/z 119.0363 and 966.0007 for negative ion mode. Polar metabolite identifications were supported by matching the retention time, accurate mass, and MS/MS fragmentation data to our in-house retention time and MS/MS library created from authentic reference standards (Mass Spectrometry Metabolite Library supplied by IROA Technologies, Millipore Sigma, St. Louis, MO, USA) and online MS/MS libraries (Human Metabolome Database (HMDB, https://hmdb.ca), Mass Bank of North America (MoNA, https://mona.fiehnlab.ucdavis.edu/), and mzCloud (https://mzcloud.org). Lipid iterative MS/MS data were annotated with the Agilent Lipid Annotator software. All data files were then analyzed in Skyline (Version 20.1.0.155) to obtain peak areas. m/z values of the metabolite and lipid target lists obtained from the metabolite identification workflow, which had at least an MS/MS match to an online library, were extracted under consideration of retention times. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002783 |
| Analysis ID: | AN002994 |
| Instrument Name: | Agilent 6540 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | gas temperature 200°C, drying gas flow 10 L/min, nebulizer pressure 44 psi, sheath gas temperature 300°C, sheath gas flow 12 L/min, VCap 3000 V, nozzle voltage 2000 V, Fragmentor 100 V, Skimmer 65 V, Oct 1 RF Vpp 750 V, and m/z range 50-1700. Data were acquired under continuous reference mass correction at m/z 121.0509 and 922.0890 for positive ion mode and m/z 119.0363 and 966.0007 for negative ion mode. Polar metabolite identifications were supported by matching the retention time, accurate mass, and MS/MS fragmentation data to our in-house retention time and MS/MS library created from authentic reference standards (Mass Spectrometry Metabolite Library supplied by IROA Technologies, Millipore Sigma, St. Louis, MO, USA) and online MS/MS libraries (Human Metabolome Database (HMDB, https://hmdb.ca), Mass Bank of North America (MoNA, https://mona.fiehnlab.ucdavis.edu/), and mzCloud (https://mzcloud.org). Lipid iterative MS/MS data were annotated with the Agilent Lipid Annotator software. All data files were then analyzed in Skyline (Version 20.1.0.155) to obtain peak areas. m/z values of the metabolite and lipid target lists obtained from the metabolite identification workflow, which had at least an MS/MS match to an online library, were extracted under consideration of retention times |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002784 |
| Analysis ID: | AN002995 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipids were detected in positive and negative ion mode with the following source parameters: gas temperature 250°C, drying gas flow 11 L/min, nebulizer pressure 35 psi, sheath gas temperature 300°C, sheath gas flow 12 L/min, VCap 3000 V, nozzle voltage 500 V, Fragmentor 160 V, Skimmer 65 V, Oct 1 RF Vpp 750 V, and m/z range 50-1700. Data were acquired under continuous reference mass correction at m/z 121.0509 and 922.0890 in positive ion mode and m/z 119.0363 and 966.0007 in negative ion mode. Polar metabolite identifications were supported by matching the retention time, accurate mass, and MS/MS fragmentation data to our in-house retention time and MS/MS library created from authentic reference standards (Mass Spectrometry Metabolite Library supplied by IROA Technologies, Millipore Sigma, St. Louis, MO, USA) and online MS/MS libraries (Human Metabolome Database (HMDB, https://hmdb.ca), Mass Bank of North America (MoNA, https://mona.fiehnlab.ucdavis.edu/), and mzCloud (https://mzcloud.org). Lipid iterative MS/MS data were annotated with the Agilent Lipid Annotator software. All data files were then analyzed in Skyline (Version 20.1.0.155) to obtain peak areas. m/z values of the metabolite and lipid target lists obtained from the metabolite identification workflow, which had at least an MS/MS match to an online library, were extracted under consideration of retention times |
| Ion Mode: | POSITIVE |
| MS ID: | MS002785 |
| Analysis ID: | AN002996 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipids were detected in positive and negative ion mode with the following source parameters: gas temperature 250°C, drying gas flow 11 L/min, nebulizer pressure 35 psi, sheath gas temperature 300°C, sheath gas flow 12 L/min, VCap 3000 V, nozzle voltage 500 V, Fragmentor 160 V, Skimmer 65 V, Oct 1 RF Vpp 750 V, and m/z range 50-1700. Data were acquired under continuous reference mass correction at m/z 121.0509 and 922.0890 in positive ion mode and m/z 119.0363 and 966.0007 in negative ion mode. Polar metabolite identifications were supported by matching the retention time, accurate mass, and MS/MS fragmentation data to our in-house retention time and MS/MS library created from authentic reference standards (Mass Spectrometry Metabolite Library supplied by IROA Technologies, Millipore Sigma, St. Louis, MO, USA) and online MS/MS libraries (Human Metabolome Database (HMDB, https://hmdb.ca), Mass Bank of North America (MoNA, https://mona.fiehnlab.ucdavis.edu/), and mzCloud (https://mzcloud.org). Lipid iterative MS/MS data were annotated with the Agilent Lipid Annotator software. All data files were then analyzed in Skyline (Version 20.1.0.155) to obtain peak areas. m/z values of the metabolite and lipid target lists obtained from the metabolite identification workflow, which had at least an MS/MS match to an online library, were extracted under consideration of retention times |
| Ion Mode: | NEGATIVE |
