Summary of Study ST001849
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001166. The data can be accessed directly via it's Project DOI: 10.21228/M80981 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
Study ID | ST001849 |
Study Title | Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity (part I) |
Study Summary | There is an urgent need to identify which COVID-19 patients will develop life-threatening illness so that medical resources can be optimally allocated and rapid treatment can be administered early in the disease course, when clinical management is most effective. To aid in the prognostic classification of disease severity, we perform untargeted metabolomics on plasma from 339 patients, with samples collected at six longitudinal time points. Using the temporal metabolic profiles and machine learning, we build a predictive model of disease severity. We discover that a panel of metabolites measured at the time of study entry successfully determine disease severity. Through analysis of longitudinal samples, we confirm that the majority of these markers are directly related to disease progression and that their levels are restored to baseline upon disease recovery. Finally, we validate that these metabolites are also altered in a hamster model of COVID-19. Our results indicate that metabolic changes associated with COVID-19 severity can be effectively used to stratify patients and inform resource allocation during the pandemic. |
Institute | Washington University in St. Louis |
Department | Chemistry |
Laboratory | Patti |
Last Name | Patti |
First Name | Gary |
Address | McMillen Chemistry Laboratory Washington University 1 Brookings Dr @ Throop Drive Rm 102 St. Louis, MO 63130-4899 |
gjpattij@wustl.edu | |
Phone | 314-935-3512 |
Submit Date | 2021-01-29 |
Num Groups | 3 |
Total Subjects | 339 |
Num Males | 184 |
Num Females | 155 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2021-06-30 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |