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 |
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 |
