#METABOLOMICS WORKBENCH estancliffe_20210128_125700 DATATRACK_ID:2432 STUDY_ID:ST001853 ANALYSIS_ID:AN003003 PROJECT_ID:000000
VERSION             	1
CREATED_ON             	June 29, 2021, 1:55 pm
#PROJECT
PR:PROJECT_TITLE                 	Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of
PR:PROJECT_TITLE                 	COVID-19 Disease Severity
PR:PROJECT_SUMMARY               	There is an urgent need to identify which COVID-19 patients will develop
PR:PROJECT_SUMMARY               	life-threatening illness so that medical resources can be optimally allocated
PR:PROJECT_SUMMARY               	and rapid treatment can be administered early in the disease course, when
PR:PROJECT_SUMMARY               	clinical management is most effective. To aid in the prognostic classification
PR:PROJECT_SUMMARY               	of disease severity, we perform untargeted metabolomics on plasma from 339
PR:PROJECT_SUMMARY               	patients, with samples collected at six longitudinal time points. Using the
PR:PROJECT_SUMMARY               	temporal metabolic profiles and machine learning, we build a predictive model of
PR:PROJECT_SUMMARY               	disease severity. We discover that a panel of metabolites measured at the time
PR:PROJECT_SUMMARY               	of study entry successfully determine disease severity. Through analysis of
PR:PROJECT_SUMMARY               	longitudinal samples, we confirm that the majority of these markers are directly
PR:PROJECT_SUMMARY               	related to disease progression and that their levels are restored to baseline
PR:PROJECT_SUMMARY               	upon disease recovery. Finally, we validate that these metabolites are also
PR:PROJECT_SUMMARY               	altered in a hamster model of COVID-19. Our results indicate that metabolic
PR:PROJECT_SUMMARY               	changes associated with COVID-19 severity can be effectively used to stratify
PR:PROJECT_SUMMARY               	patients and inform resource allocation during the pandemic.
PR:INSTITUTE                     	Washington University, St. Louis
PR:DEPARTMENT                    	Chemistry
PR:LABORATORY                    	Patti
PR:LAST_NAME                     	Patti
PR:FIRST_NAME                    	Gary
PR:ADDRESS                       	McMillen Chemistry Laboratory, Washington University 1 Brookings Dr @ Throop
PR:ADDRESS                       	Drive, Rm 102, St. Louis, MO 63130-4899
PR:EMAIL                         	gjpattij@wustl.edu
PR:PHONE                         	314-935-3512
#STUDY
ST:STUDY_TITLE                   	Longitudinal Metabolomics of Human Plasma Reveals Robust Prognostic Markers of
ST:STUDY_TITLE                   	COVID-19 Disease Severity
ST:STUDY_SUMMARY                 	There is an urgent need to identify which COVID-19 patients will develop
ST:STUDY_SUMMARY                 	life-threatening illness so that medical resources can be optimally allocated
ST:STUDY_SUMMARY                 	and rapid treatment can be administered early in the disease course, when
ST:STUDY_SUMMARY                 	clinical management is most effective. To aid in the prognostic classification
ST:STUDY_SUMMARY                 	of disease severity, we perform untargeted metabolomics on plasma from 339
ST:STUDY_SUMMARY                 	patients, with samples collected at six longitudinal time points. Using the
ST:STUDY_SUMMARY                 	temporal metabolic profiles and machine learning, we build a predictive model of
ST:STUDY_SUMMARY                 	disease severity. We discover that a panel of metabolites measured at the time
ST:STUDY_SUMMARY                 	of study entry successfully determine disease severity. Through analysis of
ST:STUDY_SUMMARY                 	longitudinal samples, we confirm that the majority of these markers are directly
ST:STUDY_SUMMARY                 	related to disease progression and that their levels are restored to baseline
ST:STUDY_SUMMARY                 	upon disease recovery. Finally, we validate that these metabolites are also
ST:STUDY_SUMMARY                 	altered in a hamster model of COVID-19. Our results indicate that metabolic
ST:STUDY_SUMMARY                 	changes associated with COVID-19 severity can be effectively used to stratify
ST:STUDY_SUMMARY                 	patients and inform resource allocation during the pandemic.
ST:INSTITUTE                     	Washington University, St. Louis
ST:DEPARTMENT                    	Chemistry
ST:LABORATORY                    	Patti
ST:LAST_NAME                     	Patti
ST:FIRST_NAME                    	Gary
ST:ADDRESS                       	McMillen Chemistry Laboratory, Washington University 1 Brookings Dr @ Throop
ST:ADDRESS                       	Drive, Rm 102, St. Louis, MO 63130-4899
ST:EMAIL                         	gjpattij@wustl.edu
ST:NUM_GROUPS                    	3
ST:TOTAL_SUBJECTS                	56
ST:NUM_FEMALES                   	56
ST:PHONE                         	314-935-3512
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mesocricetus auratus
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	-	P H-433	Group:Influenza | Day post infection:4	RAW_FILE_NAME=P H-433_polar_pos.mzML,P H-433_polar_neg.mzML,P H-433_lipid_pos.mzML,P H-433_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-457	Group:Influenza | Day post infection:4	RAW_FILE_NAME=P H-457_polar_pos.mzML,P H-457_polar_neg.mzML,P H-457_lipid_pos.mzML,P H-457_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-458	Group:Influenza | Day post infection:4	RAW_FILE_NAME=P H-458_polar_pos.mzML,P H-458_polar_neg.mzML,P H-458_lipid_pos.mzML,P H-458_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-459	Group:SARS-CoV-2 | Day post infection:14	RAW_FILE_NAME=P H-459_polar_pos.mzML,P H-459_polar_neg.mzML,P H-459_lipid_pos.mzML,P H-459_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-460	Group:Influenza | Day post infection:4	RAW_FILE_NAME=P H-460_polar_pos.mzML,P H-460_polar_neg.mzML,P H-460_lipid_pos.mzML,P H-460_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-461	Group:Influenza | Day post infection:6	RAW_FILE_NAME=P H-461_polar_pos.mzML,P H-461_polar_neg.mzML,P H-461_lipid_pos.mzML,P H-461_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-462	Group:Influenza | Day post infection:6	RAW_FILE_NAME=P H-462_polar_pos.mzML,P H-462_polar_neg.mzML,P H-462_lipid_pos.mzML,P H-462_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-463	Group:SARS-CoV-2 | Day post infection:6	RAW_FILE_NAME=P H-463_polar_pos.mzML,P H-463_polar_neg.mzML,P H-463_lipid_pos.mzML,P H-463_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-464	Group:Mock | Day post infection:4	RAW_FILE_NAME=P H-464_polar_pos.mzML,P H-464_polar_neg.mzML,P H-464_lipid_pos.mzML,P H-464_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-466	Group:Influenza | Day post infection:4	RAW_FILE_NAME=P H-466_polar_pos.mzML,P H-466_polar_neg.mzML,P H-466_lipid_pos.mzML,P H-466_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-467	Group:Influenza | Day post infection:14	RAW_FILE_NAME=P H-467_polar_pos.mzML,P H-467_polar_neg.mzML,P H-467_lipid_pos.mzML,P H-467_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-468	Group:SARS-CoV-2 | Day post infection:6	RAW_FILE_NAME=P H-468_polar_pos.mzML,P H-468_polar_neg.mzML,P H-468_lipid_pos.mzML,P H-468_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-469 -1	Group:SARS-CoV-2 | Day post infection:2	RAW_FILE_NAME=P H-469 -1_polar_pos.mzML,P H-469 -1_polar_neg.mzML,P H-469 -1_lipid_pos.mzML,P H-469 -1_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-469 -2	Group:SARS-CoV-2 | Day post infection:4	RAW_FILE_NAME=P H-469 -2 _polar_pos.mzML,P H-469 -2 _polar_neg.mzML,P H-469 -2 _lipid_pos.mzML,P H-469 -2 _lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-470	Group:Mock | Day post infection:14	RAW_FILE_NAME=P H-470_polar_pos.mzML,P H-470_polar_neg.mzML,P H-470_lipid_pos.mzML,P H-470_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-471	Group:SARS-CoV-2 | Day post infection:4	RAW_FILE_NAME=P H-471_polar_pos.mzML,P H-471_polar_neg.mzML,P H-471_lipid_pos.mzML,P H-471_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-472	Group:Mock | Day post infection:4	RAW_FILE_NAME=P H-472_polar_pos.mzML,P H-472_polar_neg.mzML,P H-472_lipid_pos.mzML,P H-472_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-473	Group:Influenza | Day post infection:14	RAW_FILE_NAME=P H-473_polar_pos.mzML,P H-473_polar_neg.mzML,P H-473_lipid_pos.mzML,P H-473_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-474	Group:Influenza | Day post infection:2	RAW_FILE_NAME=P H-474_polar_pos.mzML,P H-474_polar_neg.mzML,P H-474_lipid_pos.mzML,P H-474_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-475	Group:Mock | Day post infection:14	RAW_FILE_NAME=P H-475_polar_pos.mzML,P H-475_polar_neg.mzML,P H-475_lipid_pos.mzML,P H-475_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-476	Group:Mock | Day post infection:4	RAW_FILE_NAME=P H-476_polar_pos.mzML,P H-476_polar_neg.mzML,P H-476_lipid_pos.mzML,P H-476_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-477	Group:Influenza | Day post infection:6	RAW_FILE_NAME=P H-477_polar_pos.mzML,P H-477_polar_neg.mzML,P H-477_lipid_pos.mzML,P H-477_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-478	Group:Influenza | Day post infection:2	RAW_FILE_NAME=P H-478_polar_pos.mzML,P H-478_polar_neg.mzML,P H-478_lipid_pos.mzML,P H-478_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-479	Group:SARS-CoV-2 | Day post infection:14	RAW_FILE_NAME=P H-479_polar_pos.mzML,P H-479_polar_neg.mzML,P H-479_lipid_pos.mzML,P H-479_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-480	Group:Mock | Day post infection:4	RAW_FILE_NAME=P H-480_polar_pos.mzML,P H-480_polar_neg.mzML,P H-480_lipid_pos.mzML,P H-480_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-481	Group:Mock | Day post infection:14	RAW_FILE_NAME=P H-481_polar_pos.mzML,P H-481_polar_neg.mzML,P H-481_lipid_pos.mzML,P H-481_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-482	Group:Mock | Day post infection:4	RAW_FILE_NAME=P H-482_polar_pos.mzML,P H-482_polar_neg.mzML,P H-482_lipid_pos.mzML,P H-482_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-483	Group:Influenza | Day post infection:14	RAW_FILE_NAME=P H-483_polar_pos.mzML,P H-483_polar_neg.mzML,P H-483_lipid_pos.mzML,P H-483_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-484	Group:SARS-CoV-2 | Day post infection:14	RAW_FILE_NAME=P H-484_polar_pos.mzML,P H-484_polar_neg.mzML,P H-484_lipid_pos.mzML,P H-484_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-485	Group:SARS-CoV-2 | Day post infection:14	RAW_FILE_NAME=P H-485_polar_pos.mzML,P H-485_polar_neg.mzML,P H-485_lipid_pos.mzML,P H-485_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-486	Group:Influenza | Day post infection:6	RAW_FILE_NAME=P H-486_polar_pos.mzML,P H-486_polar_neg.mzML,P H-486_lipid_pos.mzML,P H-486_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-487	Group:SARS-CoV-2 | Day post infection:4	RAW_FILE_NAME=P H-487_polar_pos.mzML,P H-487_polar_neg.mzML,P H-487_lipid_pos.mzML,P H-487_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-488	Group:SARS-CoV-2 | Day post infection:4	RAW_FILE_NAME=P H-488_polar_pos.mzML,P H-488_polar_neg.mzML,P H-488_lipid_pos.mzML,P H-488_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-489	Group:Mock | Day post infection:14	RAW_FILE_NAME=P H-489_polar_pos.mzML,P H-489_polar_neg.mzML,P H-489_lipid_pos.mzML,P H-489_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-490	Group:Mock | Day post infection:14	RAW_FILE_NAME=P H-490_polar_pos.mzML,P H-490_polar_neg.mzML,P H-490_lipid_pos.mzML,P H-490_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-491	Group:Influenza | Day post infection:6	RAW_FILE_NAME=P H-491_polar_pos.mzML,P H-491_polar_neg.mzML,P H-491_lipid_pos.mzML,P H-491_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-492	Group:Influenza | Day post infection:2	RAW_FILE_NAME=P H-492_polar_pos.mzML,P H-492_polar_neg.mzML,P H-492_lipid_pos.mzML,P H-492_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-495	Group:SARS-CoV-2 | Day post infection:6	RAW_FILE_NAME=P H-495_polar_pos.mzML,P H-495_polar_neg.mzML,P H-495_lipid_pos.mzML,P H-495_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-496	Group:Influenza | Day post infection:14	RAW_FILE_NAME=P H-496_polar_pos.mzML,P H-496_polar_neg.mzML,P H-496_lipid_pos.mzML,P H-496_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-497	Group:Influenza | Day post infection:14	RAW_FILE_NAME=P H-497_polar_pos.mzML,P H-497_polar_neg.mzML,P H-497_lipid_pos.mzML,P H-497_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-498	Group:Influenza | Day post infection:4	RAW_FILE_NAME=P H-498_polar_pos.mzML,P H-498_polar_neg.mzML,P H-498_lipid_pos.mzML,P H-498_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-499	Group:Influenza | Day post infection:14	RAW_FILE_NAME=P H-499_polar_pos.mzML,P H-499_polar_neg.mzML,P H-499_lipid_pos.mzML,P H-499_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-501	Group:Mock | Day post infection:14	RAW_FILE_NAME=P H-501_polar_pos.mzML,P H-501_polar_neg.mzML,P H-501_lipid_pos.mzML,P H-501_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-502	Group:Influenza | Day post infection:2	RAW_FILE_NAME=P H-502_polar_pos.mzML,P H-502_polar_neg.mzML,P H-502_lipid_pos.mzML,P H-502_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-504	Group:SARS-CoV-2 | Day post infection:6	RAW_FILE_NAME=P H-504_polar_pos.mzML,P H-504_polar_neg.mzML,P H-504_lipid_pos.mzML,P H-504_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-505	Group:Influenza | Day post infection:2	RAW_FILE_NAME=P H-505_polar_pos.mzML,P H-505_polar_neg.mzML,P H-505_lipid_pos.mzML,P H-505_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-506	Group:Influenza | Day post infection:2	RAW_FILE_NAME=P H-506_polar_pos.mzML,P H-506_polar_neg.mzML,P H-506_lipid_pos.mzML,P H-506_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-507	Group:Mock | Day post infection:4	RAW_FILE_NAME=P H-507_polar_pos.mzML,P H-507_polar_neg.mzML,P H-507_lipid_pos.mzML,P H-507_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-509	Group:SARS-CoV-2 | Day post infection:6	RAW_FILE_NAME=P H-509_polar_pos.mzML,P H-509_polar_neg.mzML,P H-509_lipid_pos.mzML,P H-509_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-510	Group:SARS-CoV-2 | Day post infection:14	RAW_FILE_NAME=P H-510_polar_pos.mzML,P H-510_polar_neg.mzML,P H-510_lipid_pos.mzML,P H-510_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-511	Group:SARS-CoV-2 | Day post infection:14	RAW_FILE_NAME=P H-511_polar_pos.mzML,P H-511_polar_neg.mzML,P H-511_lipid_pos.mzML,P H-511_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-512	Group:SARS-CoV-2 | Day post infection:6	RAW_FILE_NAME=P H-512_polar_pos.mzML,P H-512_polar_neg.mzML,P H-512_lipid_pos.mzML,P H-512_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-513	Group:SARS-CoV-2 | Day post infection:2	RAW_FILE_NAME=P H-513_polar_pos.mzML,P H-513_polar_neg.mzML,P H-513_lipid_pos.mzML,P H-513_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-514	Group:SARS-CoV-2 | Day post infection:4	RAW_FILE_NAME=P H-514_polar_pos.mzML,P H-514_polar_neg.mzML,P H-514_lipid_pos.mzML,P H-514_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-515	Group:Influenza | Day post infection:6	RAW_FILE_NAME=P H-515_polar_pos.mzML,P H-515_polar_neg.mzML,P H-515_lipid_pos.mzML,P H-515_lipid_neg.mzML
SUBJECT_SAMPLE_FACTORS           	-	P H-516	Group:SARS-CoV-2 | Day post infection:2	RAW_FILE_NAME=P H-516_polar_pos.mzML,P H-516_polar_neg.mzML,P H-516_lipid_pos.mzML,P H-516_lipid_neg.mzML
#COLLECTION
CO:COLLECTION_SUMMARY            	Outbred female LVG golden Syrian hamsters (6-8 weeks of age) were obtained from
CO:COLLECTION_SUMMARY            	Charles River Laboratories (Kingston, NY). The hamsters were anesthetized by
CO:COLLECTION_SUMMARY            	intraperitoneal injection of a mixture of ketamine and xylazine prior to
CO:COLLECTION_SUMMARY            	intranasal inoculation with 0.1 mL of 1e5 plaque-forming units (PFU) of
CO:COLLECTION_SUMMARY            	SARS-CoV-2 (WA-1) or H1N1 influenza A virus (A/California/04/2009). On day 2, 4,
CO:COLLECTION_SUMMARY            	6, and 14 after infection, 3-6 anesthetized hamsters per infection group were
CO:COLLECTION_SUMMARY            	euthanized by exsanguination followed by intracardiac injection of veterinary
CO:COLLECTION_SUMMARY            	euthanasia solution (SleepAway; Fort Dodge). Plasma samples were treated by
CO:COLLECTION_SUMMARY            	exposure to germicidal UV-C light.
CO:SAMPLE_TYPE                   	Blood (plasma)
#TREATMENT
TR:TREATMENT_SUMMARY             	The hamsters were anesthetized by intraperitoneal injection of a mixture of
TR:TREATMENT_SUMMARY             	ketamine and xylazine prior to intranasal inoculation with 0.1 mL of 1e5
TR:TREATMENT_SUMMARY             	plaque-forming units (PFU) of SARS-CoV-2 (WA-1) or H1N1 influenza A virus
TR:TREATMENT_SUMMARY             	(A/California/04/2009).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Hamster plasma samples were diluted 1:4 with methanol (v/v), vortexed for 30
SP:SAMPLEPREP_SUMMARY            	seconds, and incubated at -20 C for 2 hours. Samples were centrifuged for 10
SP:SAMPLEPREP_SUMMARY            	minutes at 13,500 x g at 4°C and supernatant was transferred to a new
SP:SAMPLEPREP_SUMMARY            	centrifuge tube, concentrated, and stored at -80 C until reconstitution. Hamster
SP:SAMPLEPREP_SUMMARY            	plasma was thawed on ice. A 50 µL aliquot was transferred onto the
SP:SAMPLEPREP_SUMMARY            	solid-phase-extraction (SPE)-system CAPTIVA-EMR Lipid 96-wellplate (Agilent
SP:SAMPLEPREP_SUMMARY            	Technologies) before addition of 250 µL of acetonitrile containing 1% formic
SP:SAMPLEPREP_SUMMARY            	acid (v/v) and 10 µM internal standard (consisting of uniformly 13C and 15N
SP:SAMPLEPREP_SUMMARY            	labeled amino acids from Cambridge Isotope Laboratories, Inc). The samples were
SP:SAMPLEPREP_SUMMARY            	mixed for 1 min at 360 rpm on an orbital shaker at room temperature prior to a
SP:SAMPLEPREP_SUMMARY            	10 min incubation period at 4 C. Afterwards, 200 µL 80% acetonitrile in
SP:SAMPLEPREP_SUMMARY            	water (v/v) were added to the samples. The samples were mixed on an orbital
SP:SAMPLEPREP_SUMMARY            	shaker (360 rpm) for an additional 10 min at room temperature. The samples were
SP:SAMPLEPREP_SUMMARY            	then eluted into a 96-deepwell collection plate by centrifugation (10 min, 57 x
SP:SAMPLEPREP_SUMMARY            	g, 4 C followed by 2 min, 1000 x g, 4 C). Polar eluates were stored at -80 C
SP:SAMPLEPREP_SUMMARY            	until the day of LC/MS analysis. The SPE-plates were then washed twice with 500
SP:SAMPLEPREP_SUMMARY            	µL 80% acetonitrile in water (v/v). Lipids still bound to the SPE-material were
SP:SAMPLEPREP_SUMMARY            	then released into a second elution plate, in two elution steps applying 2x 500
SP:SAMPLEPREP_SUMMARY            	µL 1:1 methyl tert-butyl ether:methanol (v/v) onto the SPE cartridge and
SP:SAMPLEPREP_SUMMARY            	centrifuging for 2 min at 1000 g and 4 C. The combined eluates were dried under
SP:SAMPLEPREP_SUMMARY            	a stream of nitrogen (Biotage SPE Dry Evaporation System) at room temperature
SP:SAMPLEPREP_SUMMARY            	and reconstituted with 100 µL 1:1 2-propanol:methanol (v/v) prior to LC/MS
SP:SAMPLEPREP_SUMMARY            	analysis.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	An aliquot of 2 µL of lipid extract was subjected to LC/MS analysis by using an
CH:CHROMATOGRAPHY_SUMMARY        	Agilent 1290 Infinity II LC-system coupled to an Agilent 6545 Q-TOF mass
CH:CHROMATOGRAPHY_SUMMARY        	spectrometer with a dual Agilent Jet Stream electrospray ionization source.
CH:CHROMATOGRAPHY_SUMMARY        	Lipids were separated on an Acquity UPLC® HSS T3 column (2.1 x 150 mm, 1.8 µm)
CH:CHROMATOGRAPHY_SUMMARY        	including an Acquity UPLC® HSS T3 VanGuard Pre-Column (2.1 x 5mm, 1.8 µm) at a
CH:CHROMATOGRAPHY_SUMMARY        	temperature of 60 C and a flow rate of 250 µLmin-1. The mobile phases
CH:CHROMATOGRAPHY_SUMMARY        	consisted of A: 60% acetonitrile, 40% water, 0.1% formic acid, 10 mM ammonium
CH:CHROMATOGRAPHY_SUMMARY        	formate, 2.5 µM medronic acid, and B: 90% 2-propanol, 10% acetonitrile, 0.1%
CH:CHROMATOGRAPHY_SUMMARY        	formic acid, 10 mM ammonium formate (dissolved in 1 mL water). The following
CH:CHROMATOGRAPHY_SUMMARY        	linear gradient was used: 0-2 min, 30% B; 17 min, 75% B; 20 min, 85%; 23-26 min,
CH:CHROMATOGRAPHY_SUMMARY        	100% B; 26, 30% B followed by a re-equilibration phase of 5 min.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity II
CH:COLUMN_NAME                   	Acquity UPLC® HSS T3 column (2.1 x 150 mm, 1.8 µm) including an Acquity UPLC®
CH:COLUMN_NAME                   	HSS T3 VanGuard Pre-Column (2.1 x 5mm, 1.8 µm)
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6545 QTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	gas temperature 250 C, drying gas flow 11 L*min-1, nebulizer pressure 35 psi,
MS:MS_COMMENTS                   	sheath gas temperature 300 C, sheath gas flow 12 Lmin-1, VCap 3000 V, nozzle
MS:MS_COMMENTS                   	voltage 500 V, Fragmentor 160 V, Skimmer 65 V, Oct 1 RF Vpp 750 V, and m/z range
MS:MS_COMMENTS                   	50-1700. Data were acquired under continuous reference mass correction at m/z
MS:MS_COMMENTS                   	121.0509 and 922.0890 in positive ion mode and m/z 119.0363 and 966.0007 in
MS:MS_COMMENTS                   	negative ion mode. Polar metabolite identifications were supported by matching
MS:MS_COMMENTS                   	the retention time, accurate mass, and MS/MS fragmentation data to our in-house
MS:MS_COMMENTS                   	retention time and MS/MS library created from authentic reference standards
MS:MS_COMMENTS                   	(Mass Spectrometry Metabolite Library supplied by IROA Technologies, Millipore
MS:MS_COMMENTS                   	Sigma, St. Louis, MO, USA) and online MS/MS libraries (Human Metabolome Database
MS:MS_COMMENTS                   	(HMDB, https://hmdb.ca), Mass Bank of North America (MoNA,
MS:MS_COMMENTS                   	https://mona.fiehnlab.ucdavis.edu/), and mzCloud (https://mzcloud.org). Lipid
MS:MS_COMMENTS                   	iterative MS/MS data were annotated with the Agilent Lipid Annotator software.
MS:MS_COMMENTS                   	All data files were then analyzed in Skyline (Version 20.1.0.155) to obtain peak
MS:MS_COMMENTS                   	areas.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Relative Intensity
MS_METABOLITE_DATA_START
Samples	P H-433	P H-457	P H-458	P H-459	P H-460	P H-461	P H-462	P H-463	P H-464	P H-466	P H-467	P H-468	P H-469 -1	P H-469 -2	P H-470	P H-471	P H-472	P H-473	P H-474	P H-475	P H-476	P H-477	P H-478	P H-479	P H-480	P H-481	P H-482	P H-483	P H-484	P H-485	P H-486	P H-487	P H-488	P H-489	P H-490	P H-491	P H-492	P H-495	P H-496	P H-497	P H-498	P H-499	P H-501	P H-502	P H-504	P H-505	P H-506	P H-507	P H-509	P H-510	P H-511	P H-512	P H-513	P H-514	P H-515	P H-516
Factors	Group:Influenza | Day post infection:4	Group:Influenza | Day post infection:4	Group:Influenza | Day post infection:4	Group:SARS-CoV-2 | Day post infection:14	Group:Influenza | Day post infection:4	Group:Influenza | Day post infection:6	Group:Influenza | Day post infection:6	Group:SARS-CoV-2 | Day post infection:6	Group:Mock | Day post infection:4	Group:Influenza | Day post infection:4	Group:Influenza | Day post infection:14	Group:SARS-CoV-2 | Day post infection:6	Group:SARS-CoV-2 | Day post infection:2	Group:SARS-CoV-2 | Day post infection:4	Group:Mock | Day post infection:14	Group:SARS-CoV-2 | Day post infection:4	Group:Mock | Day post infection:4	Group:Influenza | Day post infection:14	Group:Influenza | Day post infection:2	Group:Mock | Day post infection:14	Group:Mock | Day post infection:4	Group:Influenza | Day post infection:6	Group:Influenza | Day post infection:2	Group:SARS-CoV-2 | Day post infection:14	Group:Mock | Day post infection:4	Group:Mock | Day post infection:14	Group:Mock | Day post infection:4	Group:Influenza | Day post infection:14	Group:SARS-CoV-2 | Day post infection:14	Group:SARS-CoV-2 | Day post infection:14	Group:Influenza | Day post infection:6	Group:SARS-CoV-2 | Day post infection:4	Group:SARS-CoV-2 | Day post infection:4	Group:Mock | Day post infection:14	Group:Mock | Day post infection:14	Group:Influenza | Day post infection:6	Group:Influenza | Day post infection:2	Group:SARS-CoV-2 | Day post infection:6	Group:Influenza | Day post infection:14	Group:Influenza | Day post infection:14	Group:Influenza | Day post infection:4	Group:Influenza | Day post infection:14	Group:Mock | Day post infection:14	Group:Influenza | Day post infection:2	Group:SARS-CoV-2 | Day post infection:6	Group:Influenza | Day post infection:2	Group:Influenza | Day post infection:2	Group:Mock | Day post infection:4	Group:SARS-CoV-2 | Day post infection:6	Group:SARS-CoV-2 | Day post infection:14	Group:SARS-CoV-2 | Day post infection:14	Group:SARS-CoV-2 | Day post infection:6	Group:SARS-CoV-2 | Day post infection:2	Group:SARS-CoV-2 | Day post infection:4	Group:Influenza | Day post infection:6	Group:SARS-CoV-2 | Day post infection:2
Cer_NS d18:1_16:0	254263	338849	148495	269975	358078	247441	182812	248128	276197	576899	275332	216990	362849	276684	229309	188073	209832	211748	237251	228607	390029	361735	347434	170321	341832	259747	238260	322755	286627	251894	399423	390744	197281	254991	257959	170617	415055	273645	260668	248765	207894	239111	294522	392768	358476	488211	266364	174129	316397	196582	210051	176058	408851	297508	250234	289705
LPC 18:2/0:0	578418240	911317248	801721728	1125390080	872803712	1137050624	1111922688	968802304	1119400704	1073702528	891318208	1090295168	1134288000	955946432	833977024	928133312	1078359808	970661184	1078633088	973532864	1175225344	1123546496	1120357376	971301184	1135108992	964439232	907638720	1114620416	996172480	1026803968	1098875776	542429504	832621184	1009140736	966559744	997369280	968036288	996107264	1152047744	1121969280	891428416	1130332032	921211264	937638976	951064384	988608256	1045766912	903860608	985089344	889221248	1013376256	1083412608	1015451968	725445312	917849920	1105954048
LPC 18:0/0:0	597503104	853489216	861625216	825121024	1034325632	882868032	1159614464	873599232	1089117056	880207744	763800896	934184448	1165932416	1031901504	858973248	830878016	1005041792	888512256	1148513408	1007942080	1152252672	1022445632	1160473600	802190656	995284864	1077072512	933992640	926503360	822235840	719038272	1111214848	898249664	893475968	855351744	891364288	959977664	919765952	831865600	889480512	986933760	893643584	990818944	872441088	992937280	905376960	1152856192	1100822272	955756032	1043870400	811032384	829679808	1052327552	915407744	745802560	828069120	1150666880
LPC 18:1/0:0	365801056	594430016	506042912	915069248	570706624	1028225152	982430016	687404864	958847808	793419520	701412672	867946816	842502144	607129408	486218464	497632800	877117056	751756160	660546432	640029056	1109343744	975792384	761865472	649821120	1031407872	677229824	617308096	936125376	770905984	749040448	1003933056	244921824	446340960	928684544	701693696	763589760	750518464	703308480	953737216	1063614272	644831744	974461760	581005696	747145536	698019904	730570048	836028800	624217920	569749824	574435712	704298304	634251200	708909312	331547136	683869248	872845440
LPC 20:4/0:0	140709952	248640704	286603040	325806976	236002336	314764224	382756480	271392896	313667744	291243072	254385888	330639168	327076896	361985472	197841888	287601856	331287232	305904416	406260064	333552672	413692384	344447872	338342016	238550272	373351744	262157872	323350592	303690752	271071616	267525312	382974432	318110368	241523056	276681280	266693920	295195264	300858016	296800544	327785984	394664864	292348800	377783904	265961840	311895104	279881024	369250144	342359808	300876736	261733056	246410304	263534496	366535232	270502432	181906480	272069984	328309312
LPC 0:0/16:0	219307536	435038784	372533472	495196640	425404672	557875072	534394624	483557920	563380416	522313568	427876800	516675168	494085056	409103744	376360960	376621920	584242880	453636096	489336448	473999488	629655616	507850560	541204352	439380608	573105536	484669568	454087648	552469824	410214720	391129920	510995232	374807456	335657216	542142272	469781632	465370208	454251648	453669024	559949376	518192896	443550720	516039040	459772480	450164256	453980768	477940928	499013664	426785376	438891680	352907584	406271264	419827360	447858656	263299040	418865088	460014592
LPC 16:0/0:0	827090432	1137591424	1047973760	1247890560	1117744640	1304097664	1268717184	1202875136	1307764608	1240885376	1147135104	1253974144	1234143360	1103850752	1049488704	1064127552	1302893312	1176926208	1201161344	1186788736	1395116032	1236240384	1256587008	1141635456	1298271232	1183319808	1162646912	1293089152	1109902592	1106019584	1242665856	1035554048	994320000	1277241216	1199760768	1206704384	1163626880	1169409664	1297134848	1257552768	1149563648	1268695808	1159248512	1164400768	1172723968	1192379776	1215525376	1145636864	1163040768	1044841856	1112999680	1128998272	1160771968	900866432	1138577280	1196272768
LPC 0:0/18:0	108745104	210460528	212340048	193363648	268271456	195124080	333212704	196742496	315035264	211993664	156548768	223495984	370883008	283255904	208670752	192034144	250545680	225308448	321951456	273433664	344960640	262132096	330205344	184720256	246685120	288809536	244201520	220802384	187274336	153483440	303990880	212041008	215053744	185762944	222180496	238936352	221394624	192481952	200455664	250094736	219302256	262658272	208366992	259114528	210193568	316033312	297157664	242866960	286687968	177483920	184679584	287274784	222458176	152495344	181722768	337654272
LPC 16:1/0:0	27396354	41870536	51146616	77802280	60472400	112645104	78151936	73628736	100996280	58163632	74588488	84575920	72545968	51257176	41421988	41245764	107410936	89705616	57752952	50229888	114424344	93813104	70303920	66000092	86961480	55799584	60811216	91285256	63447444	52171112	104701440	18788782	44723772	111905000	72761112	57059880	73007704	75464464	80043416	125985992	84402896	91863880	44015760	105191568	58076620	68063056	85087080	63180060	43738196	46841636	44855780	49855736	71635600	25178090	63869216	67937472
LPC 17:0/0:0	37923008	57661236	82023824	59030424	59974948	66944860	82088288	61873060	75325760	65435220	54995400	75400368	83933136	62922640	83990640	63786236	64702004	64945016	96703144	80136272	98360800	62089468	71987928	64344028	56963444	83341384	72369288	50863472	49183352	49516872	65848840	48336868	56178904	55904032	66991116	79050320	54066256	56447632	59203048	57636560	79178632	72519408	70858928	72382432	57167292	69703008	65594516	78097144	67686288	43737856	56559064	87424120	66101244	50081620	62519984	71047888
LPC 20:3/0:0	19776628	41586752	35789336	68395352	39659668	66798436	84017416	39377500	69026312	51141624	45761668	58814888	73627744	62493516	23016058	41055424	75557752	55831788	76664056	58936940	95989096	74383768	70305728	41842416	90888032	36185340	55476344	67189296	49893932	54010964	90770232	16573480	29972712	54508400	44683704	56673728	57395512	52022512	76696720	100295520	44539328	89075592	39799324	54716072	46203580	74041792	73194240	47647796	43561752	41399712	48646452	60870604	46891416	19350550	49947804	65643108
LPC 20:2/0:0	13742236	33540566	20096488	46496928	26868282	43210860	55161452	25611224	47096536	35365988	33320736	34055400	48631724	30925114	19265148	21829172	41972304	30979396	39177740	32503762	61522188	46327412	38290092	25815582	58157372	25926238	30966386	43172100	29193346	34776276	57702484	6126602	19054980	35148760	27952070	37021688	33905592	27880664	50947612	62817492	25999404	57331048	29836380	33585272	22601204	46874912	45621520	30120472	26667098	20447414	31444508	32775092	28753754	12212919	30929044	43481244
LPC 14:0/0:0	11363385	19903580	14398058	22687516	19154584	28388220	36174428	15020375	27693670	24074622	22071994	20122946	20772752	14474736	14225460	13106789	35842236	21653150	26081956	22259858	38670716	28462468	26761686	19797720	36393192	22452422	21092918	26199334	18889862	14505290	28595674	4549388	9496055	30386588	21625898	25331254	18322346	21483008	28355932	32003814	22742158	28467758	17512860	25406554	15875677	21314270	24486806	25817214	10931109	13778306	14636942	15549986	16204788	7994703	23010886	19880106
PC 38:6	17771774	16678404	19271692	22359820	12673147	28281322	24418696	16145294	22826034	18118424	22197302	22045346	4956395	11414523	11983366	10678878	16974996	21736670	10742377	15001309	31553548	24432890	16657365	8345140	19546340	21421886	19955752	20209862	17509756	17860196	30491456	7069394	8522772	18785942	21401044	21432112	15110967	17516290	21079398	28474170	19394438	28895178	14903794	24411258	18072002	21398756	18514580	19339788	6252755	10159738	14642579	19102178	19335750	10062041	16401026	25492798
PC 18:2_22:6	13419641	14080592	24320842	18721814	15380894	18931786	26493088	23084176	23511922	14644991	14639470	23784212	39053684	16873176	16594439	16546222	16220788	23116774	23593226	19786370	25792008	19912450	20373964	20259102	19916084	29222254	25140594	12886388	18953000	15712073	28802012	8970259	10955366	16159997	18159644	18576402	16971742	21942254	15750219	28860044	21296476	25905614	15256595	23679374	22249696	27607222	27100870	22679172	17830408	19295924	15478288	28042352	22840594	11439129	14883133	32390620
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name
Cer_NS d18:1_16:0
LPC 18:2/0:0
LPC 18:0/0:0
LPC 18:1/0:0
LPC 20:4/0:0
LPC 0:0/16:0
LPC 16:0/0:0
LPC 0:0/18:0
LPC 16:1/0:0
LPC 17:0/0:0
LPC 20:3/0:0
LPC 20:2/0:0
LPC 14:0/0:0
PC 38:6
PC 18:2_22:6
METABOLITES_END
#END