Summary of Study ST002194

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 PR001398. The data can be accessed directly via it's Project DOI: 10.21228/M8141Z 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	ST002194
Study Title	Metabolic profiling at COVID-19 onset shows disease severity and sex-specific dysregulation
Study Summary	In this study CE-MS and GC-MS based metabolomics was used to analyze COVID-19 disease. In total, 144 individuals classified as healthy, asymptomatic/mils, moderate and severe according to the highest COVID-19 severity status, were analyzed.
Institute	CEMBIO
Last Name	Barbas
First Name	Coral
Address	CEU Universities, Urbanización Montepríncipe
Email	cbarbas@ceu.es
Phone	+34 913724700
Submit Date	2022-06-09
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	GC-MS/LC-MS
Release Date	2022-06-17
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001398
Project DOI:	doi: 10.21228/M8141Z
Project Title:	Metabolic profiling at COVID-19 onset shows disease severity and sex-specific dysregulation
Project Summary:	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an acute respiratory disease, the coronavirus disease 2019 (COVID-19), which has been associated with high mortality and morbidity rates worldwide. However, the biological mechanisms of SARS-CoV-2 induced pathology are still not completely understood. This study aimed to characterize the metabolic and cytokine profile of COVID-19 patients at hospital admission and identify its association with the highest COVID-19 severity reached, as well as the differences by sex. We performed a metabolomics analysis in 129 COVID-19 patients enrolled from March to September 2020 at three hospitals in Madrid: Infanta Leonor University Hospital, del Tajo University Hospital, and Príncipe de Asturias University Hospital (although 123 fulfilled criteria and were used in statistical analysis), and a control group of 15 pre-pandemic healthy controls without any known infection. Patient samples were collected at hospital admission or within the first days after hospitalization and an untargeted plasma metabolic profiling (gas chromatography and capillary electrophoresis-mass spectrometry (GC and CE-MS)) was performed. The primary outcomes were SARS-CoV-2 infection (COVID-19 patients versus healthy controls), COVID-19 symptomatology (hospitalized symptomatic patients (moderate plus severe) versus asymptomatic), and COVID-19 severe (severe versus moderate).
Institute:	CEMBIO
Last Name:	Barbas
First Name:	Coral
Address:	CEU Universities, Urbanización Montepríncipe
Email:	cbarbas@ceu.es
Phone:	+34 913724700

Subject:

Subject ID:	SU002280
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Label	Gender	HTA	Obesity	Dyspnoea
SA210285	HUPA_83	AM	0	0	0	0
SA210286	HUPA_65	AM	0	0	0	0
SA210287	HUPA_93	AM	0	0	0	0
SA210288	HUPA_78	AM	0	0	0	0
SA210289	HUPA_73	AM	0	1	0	0
SA210290	HUPA_77_Bis	AM	0	1	0	0
SA210291	HUPA_76	AM	0	1	1	0
SA210292	HT_12	AM	0	1	2	0
SA210293	HUPA_81	AM	1	0	0	0
SA210294	HUPA_85	AM	1	0	0	1
SA210295	HUPA_67	AM	1	0	1	0
SA210296	HUPA_97	AM	1	1	0	0
SA210297	CS_84	Healthy	0	NA	NA	NA
SA210298	CS_86	Healthy	0	NA	NA	NA
SA210299	CS_87	Healthy	0	NA	NA	NA
SA210300	CS_78	Healthy	0	NA	NA	NA
SA210301	CS_42	Healthy	0	NA	NA	NA
SA210302	CS_66	Healthy	0	NA	NA	NA
SA210303	CS_11	Healthy	0	NA	NA	NA
SA210304	CS_79	Healthy	0	NA	NA	NA
SA210305	CS_54	Healthy	1	NA	NA	NA
SA210306	CS_55	Healthy	1	NA	NA	NA
SA210307	CS_5	Healthy	1	NA	NA	NA
SA210308	CS_48	Healthy	1	NA	NA	NA
SA210309	CS_15	Healthy	1	NA	NA	NA
SA210310	CS_77	Healthy	1	NA	NA	NA
SA210311	CS_41	Healthy	1	NA	NA	NA
SA210312	CNMI_47	Moderate	0	0	0	0
SA210313	CNMI_26	Moderate	0	0	0	0
SA210314	CNMI_17	Moderate	0	0	0	0
SA210315	CNMI_16	Moderate	0	0	0	1
SA210316	CNMI_317	Moderate	0	0	0	1
SA210317	CNMI_43	Moderate	0	0	0	1
SA210318	CNMI_617	Moderate	0	0	0	1
SA210319	CNMI_42	Moderate	0	0	0	1
SA210320	CNMI_53	Moderate	0	0	0	1
SA210321	CNMI_52	Moderate	0	0	0	1
SA210322	CNMI_19	Moderate	0	0	0	1
SA210323	CNMI_12	Moderate	0	0	0	1
SA210324	CNMI_21	Moderate	0	0	0	1
SA210325	CNMI_9	Moderate	0	0	0	1
SA210326	CNMI_48	Moderate	0	1	0	0
SA210327	CNMI_611	Moderate	0	1	0	0
SA210328	CNMI_20_Bis	Moderate	0	1	0	0
SA210329	CNMI_76	Moderate	0	1	0	0
SA210330	CNMI_61	Moderate	0	1	0	1
SA210331	CNMI_55	Moderate	0	1	0	1
SA210332	CNMI_56	Moderate	0	1	0	1
SA210333	CNMI_75	Moderate	0	1	0	1
SA210334	CNMI_25	Moderate	0	1	0	1
SA210335	CNMI_44	Moderate	0	1	0	1
SA210336	CNMI_24	Moderate	0	1	0	1
SA210337	CNMI_46	Moderate	0	1	0	1
SA210338	CNMI_32	Moderate	0	1	1	0
SA210339	CNMI_93_Bis	Moderate	0	1	1	0
SA210340	CNMI_68	Moderate	0	1	1	1
SA210341	CNMI_86	Moderate	0	1	1	1
SA210342	CNMI_41	Moderate	1	0	0	0
SA210343	CNMI_51	Moderate	1	0	0	0
SA210344	CNMI_27	Moderate	1	0	0	0
SA210345	CNMI_2	Moderate	1	0	0	0
SA210346	CNMI_18	Moderate	1	0	0	0
SA210347	CNMI_30	Moderate	1	0	0	0
SA210348	CNMI_36	Moderate	1	0	0	0
SA210349	CNMI_63	Moderate	1	0	0	0
SA210350	CNMI_64	Moderate	1	0	0	0
SA210351	CNMI_87	Moderate	1	0	0	1
SA210352	CNMI_90	Moderate	1	0	0	1
SA210353	CNMI_34_Bis	Moderate	1	0	0	1
SA210354	CNMI_39	Moderate	1	0	0	1
SA210355	CNMI_1	Moderate	1	0	0	1
SA210356	CNMI_22	Moderate	1	0	0	1
SA210357	CNMI_5	Moderate	1	0	0	1
SA210358	CNMI_71	Moderate	1	0	0	1
SA210359	CNMI_14	Moderate	1	0	0	1
SA210360	CNMI_95	Moderate	1	0	0	1
SA210361	CNMI_73	Moderate	1	0	0	1
SA210362	CNMI_4	Moderate	1	0	1	0
SA210363	CNMI_28	Moderate	1	0	1	1
SA210364	CNMI_246	Moderate	1	0	1	1
SA210365	CNMI_59	Moderate	1	1	0	0
SA210366	CNMI_31	Moderate	1	1	0	0
SA210367	CNMI_29	Moderate	1	1	0	0
SA210368	CNMI_89	Moderate	1	1	0	0
SA210369	CNMI_45	Moderate	1	1	0	1
SA210370	CNMI_58	Moderate	1	1	0	1
SA210371	CNMI_13	Moderate	1	1	0	1
SA210372	CNMI_91	Moderate	1	1	0	1
SA210373	CNMI_6	Moderate	1	1	0	1
SA210374	CNMI_78	Moderate	1	1	1	1
SA210375	CNMI_72	Moderate	1	1	1	1
SA210376	HT_5	NA	NA	NA	NA	NA
SA210377	HT_1	NA	NA	NA	NA	NA
SA210378	CNMI_0810	NA	NA	NA	NA	NA
SA210379	HT_2	NA	NA	NA	NA	NA
SA210380	HT_3	NA	NA	NA	NA	NA
SA210381	HT_4	NA	NA	NA	NA	NA
SA210382	HT_26	Severe	0	0	0	0
SA210383	HT_20	Severe	0	0	0	1
SA210384	CNMI_54	Severe	0	0	0	1

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Collection:

Collection ID:	CO002273
Collection Summary:	Samples were collected at hospital admission or within the first days after hospitalization (median = 2 days) and before treatment with immunotherapy against IL-6 (e.g., tocilizumab), interferon beta, corticoids, or ribavirin, among others. Plasma samples were obtained after centrifugation blood in EDTA tubes and stored at -80 °C.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002292
Treatment Summary:	Plasma samples were inactivated with cold (-20°C) MeOH : EtOH (1:1, v/v) and vortex-mixed for 1 min, incubated on ice for 5 min, and centrifuged for 20 min at 16000 xg at 4°C. The resulting supernatant was stored at -80°C until analysis. Due to the broad differences in physical-chemical properties of metabolites, we used GC-MS (focused on small molecules that can be made volatile by derivatization) and CE-MS (focused on polar and ionic compounds) in order to increase the metabolite coverage. Sample preparation for GC-MS and CE-MS was detailed in the uploaded file in sample preparation part.
Treatment Protocol Filename:	Sample_treatment.pdf

Sample Preparation:

Sampleprep ID:	SP002286
Sampleprep Summary:	For GC-MS analysis samples, 200 µL of frozen plasma supernatant was thawed at room temperature and 30 µL of 80 mg/L deuterated palmitic acid in MeOH was added as internal standard (IS). After samples were evaporated to dryness a two-step derivatization process was done. For CE-MS analysis, 200 µL of frozen supernatant was thawed until room temperature and it was evaporated to dryness using a SpeedVac Concentrator System (Thermo Fisher Scientific, MA). Afterwards, 100 µL of 0.2 mM methionine sulfone (MetS) as internal standard (IS) in 0.1 M formic acid solution was added. Samples were vortex mixed, filtered and subsequently centrifuged. More detailed information is included in the attached pdf.

Sampleprep ID:

SP002286

Sampleprep Summary:

For GC-MS analysis samples, 200 µL of frozen plasma supernatant was thawed at room temperature and 30 µL of 80 mg/L deuterated palmitic acid in MeOH was added as internal standard (IS). After samples were evaporated to dryness a two-step derivatization process was done. For CE-MS analysis, 200 µL of frozen supernatant was thawed until room temperature and it was evaporated to dryness using a SpeedVac Concentrator System (Thermo Fisher Scientific, MA). Afterwards, 100 µL of 0.2 mM methionine sulfone (MetS) as internal standard (IS) in 0.1 M formic acid solution was added. Samples were vortex mixed, filtered and subsequently centrifuged. More detailed information is included in the attached pdf.

Combined analysis:

Analysis ID	AN003591	AN003592
Analysis type	MS	MS
Chromatography type	CE	GC
Chromatography system	Agilent 7100 CE	8890
Column	silica capillary (100 cm; inner diameter,50um,Agilent Technologies)	Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type	ESI	EI
MS instrument type	TOF	Single quadrupole
MS instrument name	Agilent CE-TOFMS	Agilent 5977B
Ion Mode	POSITIVE	UNSPECIFIED
Units	Peak Area	Corrected areas

Chromatography:

Chromatography ID:	CH002653
Chromatography Summary:	Metabolite separation was performed in a fused silica capillary (100 cm; inner diameter, 50 µm, Agilent Technologies). Before each analysis, background electrolyte (BFE) (0.8 M formic acid solution in 10 % MeOH; v/v) was flushed for 5 min (950 mbar). Samples injections were performed over 50 s at 50 mbar and BGE was injected after each injection for 10 s at 100 mbar to improve reproducibility. The separation was carried out with an internal pressure of 25 mbar and 30 kV voltage with a total analytical run time of 35 min.
Methods Filename:	Sample_Analysis.pdf
Instrument Name:	Agilent 7100 CE
Column Name:	silica capillary (100 cm; inner diameter,50um,Agilent Technologies)
Chromatography Type:	CE

Chromatography ID:	CH002654
Chromatography Summary:	The flow rate of helium carrier gas was constant at 1.1359 mL/min and the injector temperature was set at 250 °C. The lock of the retention time (RTL) relative to the internal standard (methyl stearate) peak at 19.66 min was performed. The oven temperature gradient was initially set at 60 °C and was maintained for 1 min. Then it was raised by 10 °C/min until it reached 325 °C, and then was held at this temperature for 10 min before cooling down. The total analysis run time was 37.5 min.
Methods Filename:	Sample_Analysis.pdf
Instrument Name:	8890
Column Name:	Agilent DB5-MS (30m x 0.25mm, 0.25um)
Chromatography Type:	GC

MS:

MS ID:	MS003346
Analysis ID:	AN003591
Instrument Name:	Agilent CE-TOFMS
Instrument Type:	TOF
MS Type:	ESI
MS Comments:	Data were acquired in positive ionization polarity with a full scan range from 70 to 1000 m/z at a rate of 1.36 scan/s. The rest of MS conditions were: fragmentor set to 125 V, skimmer to 65 V, OCT RF Vpp to 750 V, drying gas temperature to 200 °C, flow rate to 10 L/min, nebulizer to 10 psig, and capillary voltage to 3500 V. The sheath liquid used for detection contained two reference masses (5 µL of purine with m/z 121.0509 and 5 µL of HP-0921 with m/z 922.0098) in MeOH/water (1/1; v/v) with 1 mM formic acid and the flow rate was set to 0.6 mL/min (split 1:100). The data acquisition was made using the Agilent MassHunter Workstation (Agilent Technologies).
Ion Mode:	POSITIVE
Analysis Protocol File:	Sample_Analysis.pdf

MS ID:	MS003347
Analysis ID:	AN003592
Instrument Name:	Agilent 5977B
Instrument Type:	Single quadrupole
MS Type:	EI
MS Comments:	The transfer line temperature was stablished at 280 °C and the electron ionization (EI) source was operated at 70 eV and the filament source temperature was set at 200 °C. Mass spectra were collected over a mass range of 50 - 600 m/z at a scan rate of 2.7 scans/s. Data were acquired using the Agilent MassHunter Workstation GC/MS Data Acquisition (version 10.0).
Ion Mode:	UNSPECIFIED
Analysis Protocol File:	Sample_Analysis.pdf