Summary of Study ST001853

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	ST001853
Study Title	Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity (Part 2)
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
Email	gjpattij@wustl.edu
Phone	314-935-3512
Submit Date	2021-01-28
Num Groups	3
Total Subjects	56
Num Females	56
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:

Project:

Project ID:	PR001166
Project DOI:	doi: 10.21228/M80981
Project Title:	Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of COVID-19 Disease Severity
Project 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
Email:	gjpattij@wustl.edu
Phone:	314-935-3512

Subject:

Subject ID:	SU001930
Subject Type:	Mammal
Subject Species:	Mesocricetus auratus
Taxonomy ID:	10036

Factors:

Subject type: Mammal; Subject species: Mesocricetus auratus (Factor headings shown in green)

mb_sample_id	local_sample_id	Group	Day post infection
SA174153	P H-473	Influenza	14
SA174154	P H-497	Influenza	14
SA174155	P H-499	Influenza	14
SA174156	P H-496	Influenza	14
SA174157	P H-467	Influenza	14
SA174158	P H-483	Influenza	14
SA174159	P H-502	Influenza	2
SA174160	P H-505	Influenza	2
SA174161	P H-492	Influenza	2
SA174162	P H-506	Influenza	2
SA174163	P H-474	Influenza	2
SA174164	P H-478	Influenza	2
SA174165	P H-457	Influenza	4
SA174166	P H-458	Influenza	4
SA174167	P H-460	Influenza	4
SA174168	P H-433	Influenza	4
SA174169	P H-466	Influenza	4
SA174170	P H-498	Influenza	4
SA174171	P H-486	Influenza	6
SA174172	P H-477	Influenza	6
SA174173	P H-491	Influenza	6
SA174174	P H-462	Influenza	6
SA174175	P H-461	Influenza	6
SA174176	P H-515	Influenza	6
SA174177	P H-501	Mock	14
SA174178	P H-490	Mock	14
SA174179	P H-489	Mock	14
SA174180	P H-475	Mock	14
SA174181	P H-470	Mock	14
SA174182	P H-481	Mock	14
SA174183	P H-507	Mock	4
SA174184	P H-464	Mock	4
SA174185	P H-472	Mock	4
SA174186	P H-482	Mock	4
SA174187	P H-476	Mock	4
SA174188	P H-480	Mock	4
SA174189	P H-510	SARS-CoV-2	14
SA174190	P H-511	SARS-CoV-2	14
SA174191	P H-484	SARS-CoV-2	14
SA174192	P H-459	SARS-CoV-2	14
SA174193	P H-485	SARS-CoV-2	14
SA174194	P H-479	SARS-CoV-2	14
SA174195	P H-513	SARS-CoV-2	2
SA174196	P H-516	SARS-CoV-2	2
SA174197	P H-469 -1	SARS-CoV-2	2
SA174198	P H-514	SARS-CoV-2	4
SA174199	P H-469 -2	SARS-CoV-2	4
SA174200	P H-488	SARS-CoV-2	4
SA174201	P H-471	SARS-CoV-2	4
SA174202	P H-487	SARS-CoV-2	4
SA174203	P H-463	SARS-CoV-2	6
SA174204	P H-509	SARS-CoV-2	6
SA174205	P H-504	SARS-CoV-2	6
SA174206	P H-495	SARS-CoV-2	6
SA174207	P H-468	SARS-CoV-2	6
SA174208	P H-512	SARS-CoV-2	6

Showing results 1 to 56 of 56

Showing results 1 to 56 of 56

Collection:

Collection ID:	CO001923
Collection Summary:	Outbred female LVG golden Syrian hamsters (6-8 weeks of age) were obtained from Charles River Laboratories (Kingston, NY). The hamsters were anesthetized by intraperitoneal injection of a mixture of ketamine and xylazine prior to intranasal inoculation with 0.1 mL of 1e5 plaque-forming units (PFU) of SARS-CoV-2 (WA-1) or H1N1 influenza A virus (A/California/04/2009). On day 2, 4, 6, and 14 after infection, 3-6 anesthetized hamsters per infection group were euthanized by exsanguination followed by intracardiac injection of veterinary euthanasia solution (SleepAway; Fort Dodge). Plasma samples were treated by exposure to germicidal UV-C light.
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR001942
Treatment Summary:	The hamsters were anesthetized by intraperitoneal injection of a mixture of ketamine and xylazine prior to intranasal inoculation with 0.1 mL of 1e5 plaque-forming units (PFU) of SARS-CoV-2 (WA-1) or H1N1 influenza A virus (A/California/04/2009).

Sample Preparation:

Sampleprep ID:	SP001936
Sampleprep Summary:	Hamster plasma samples were diluted 1:4 with methanol (v/v), vortexed for 30 seconds, and incubated at -20 C for 2 hours. Samples were centrifuged for 10 minutes at 13,500 x g at 4°C and supernatant was transferred to a new centrifuge tube, concentrated, and stored at -80 C until reconstitution. Hamster plasma 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.

Sampleprep ID:

SP001936

Sampleprep Summary:

Hamster plasma samples were diluted 1:4 with methanol (v/v), vortexed for 30 seconds, and incubated at -20 C for 2 hours. Samples were centrifuged for 10 minutes at 13,500 x g at 4°C and supernatant was transferred to a new centrifuge tube, concentrated, and stored at -80 C until reconstitution. Hamster plasma 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.

Combined analysis:

Analysis ID	AN003001	AN003002	AN003003	AN003004
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) including a ZIC-pHILIC guard (2.1 mm x 20 mm,5um)	SeQuant ZIC-pHILIC (100 x 2.1mm,5um) including a ZIC-pHILIC guard (2.1 mm x 20 mm,5um)	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) including an Acquity UPLC® HSS T3 VanGuard Pre-Column (2.1 x 5mm,1.8 µm)	Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) including an Acquity UPLC® HSS T3 VanGuard Pre-Column (2.1 x 5mm,1.8 µm)
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:	CH002226
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-1. 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 400 µLmin-1 and 2 min at 250 µLmin-1.
Instrument Name:	Agilent 1290 Infinity II
Column Name:	SeQuant ZIC-pHILIC (100 x 2.1mm,5um) including a ZIC-pHILIC guard (2.1 mm x 20 mm,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:	CH002227
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-1. 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) including an Acquity UPLC® HSS T3 VanGuard Pre-Column (2.1 x 5mm,1.8 µm)
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:	MS002790
Analysis ID:	AN003001
Instrument Name:	Agilent 6540 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	gas temperature 200 C, drying gas flow 10 Lmin-1, nebulizer pressure 44 psi, sheath gas temperature 300 C, sheath gas flow 12 Lmin-1, 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.
Ion Mode:	POSITIVE

MS ID:	MS002791
Analysis ID:	AN003002
Instrument Name:	Agilent 6540 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	gas temperature 200 C, drying gas flow 10 Lmin-1, nebulizer pressure 44 psi, sheath gas temperature 300 C, sheath gas flow 12 Lmin-1, 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.
Ion Mode:	NEGATIVE

MS ID:	MS002792
Analysis ID:	AN003003
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	gas temperature 250 C, drying gas flow 11 Lmin-1, nebulizer pressure 35 psi, sheath gas temperature 300 C, sheath gas flow 12 Lmin-1, 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.
Ion Mode:	POSITIVE

MS ID:	MS002793
Analysis ID:	AN003004
Instrument Name:	Agilent 6545 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	gas temperature 250 C, drying gas flow 11 Lmin-1, nebulizer pressure 35 psi, sheath gas temperature 300 C, sheath gas flow 12 Lmin-1, 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.
Ion Mode:	NEGATIVE