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.

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Study IDST002194
Study TitleMetabolic profiling at COVID-19 onset shows disease severity and sex-specific dysregulation
Study SummaryIn 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 NameBarbas
First NameCoral
AddressCEU Universities, Urbanización Montepríncipe
Emailcbarbas@ceu.es
Phone+34 913724700
Submit Date2022-06-09
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailGC/LC-MS
Release Date2022-06-17
Release Version1
Coral Barbas Coral Barbas
https://dx.doi.org/10.21228/M8141Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA210285HUPA_83AM 0 0 0 0
SA210286HUPA_65AM 0 0 0 0
SA210287HUPA_93AM 0 0 0 0
SA210288HUPA_78AM 0 0 0 0
SA210289HUPA_73AM 0 1 0 0
SA210290HUPA_77_BisAM 0 1 0 0
SA210291HUPA_76AM 0 1 1 0
SA210292HT_12AM 0 1 2 0
SA210293HUPA_81AM 1 0 0 0
SA210294HUPA_85AM 1 0 0 1
SA210295HUPA_67AM 1 0 1 0
SA210296HUPA_97AM 1 1 0 0
SA210297CS_84Healthy 0 NA NA NA
SA210298CS_86Healthy 0 NA NA NA
SA210299CS_87Healthy 0 NA NA NA
SA210300CS_78Healthy 0 NA NA NA
SA210301CS_42Healthy 0 NA NA NA
SA210302CS_66Healthy 0 NA NA NA
SA210303CS_11Healthy 0 NA NA NA
SA210304CS_79Healthy 0 NA NA NA
SA210305CS_54Healthy 1 NA NA NA
SA210306CS_55Healthy 1 NA NA NA
SA210307CS_5Healthy 1 NA NA NA
SA210308CS_48Healthy 1 NA NA NA
SA210309CS_15Healthy 1 NA NA NA
SA210310CS_77Healthy 1 NA NA NA
SA210311CS_41Healthy 1 NA NA NA
SA210312CNMI_47Moderate 0 0 0 0
SA210313CNMI_26Moderate 0 0 0 0
SA210314CNMI_17Moderate 0 0 0 0
SA210315CNMI_16Moderate 0 0 0 1
SA210316CNMI_317Moderate 0 0 0 1
SA210317CNMI_43Moderate 0 0 0 1
SA210318CNMI_617Moderate 0 0 0 1
SA210319CNMI_42Moderate 0 0 0 1
SA210320CNMI_53Moderate 0 0 0 1
SA210321CNMI_52Moderate 0 0 0 1
SA210322CNMI_19Moderate 0 0 0 1
SA210323CNMI_12Moderate 0 0 0 1
SA210324CNMI_21Moderate 0 0 0 1
SA210325CNMI_9Moderate 0 0 0 1
SA210326CNMI_48Moderate 0 1 0 0
SA210327CNMI_611Moderate 0 1 0 0
SA210328CNMI_20_BisModerate 0 1 0 0
SA210329CNMI_76Moderate 0 1 0 0
SA210330CNMI_61Moderate 0 1 0 1
SA210331CNMI_55Moderate 0 1 0 1
SA210332CNMI_56Moderate 0 1 0 1
SA210333CNMI_75Moderate 0 1 0 1
SA210334CNMI_25Moderate 0 1 0 1
SA210335CNMI_44Moderate 0 1 0 1
SA210336CNMI_24Moderate 0 1 0 1
SA210337CNMI_46Moderate 0 1 0 1
SA210338CNMI_32Moderate 0 1 1 0
SA210339CNMI_93_BisModerate 0 1 1 0
SA210340CNMI_68Moderate 0 1 1 1
SA210341CNMI_86Moderate 0 1 1 1
SA210342CNMI_41Moderate 1 0 0 0
SA210343CNMI_51Moderate 1 0 0 0
SA210344CNMI_27Moderate 1 0 0 0
SA210345CNMI_2Moderate 1 0 0 0
SA210346CNMI_18Moderate 1 0 0 0
SA210347CNMI_30Moderate 1 0 0 0
SA210348CNMI_36Moderate 1 0 0 0
SA210349CNMI_63Moderate 1 0 0 0
SA210350CNMI_64Moderate 1 0 0 0
SA210351CNMI_87Moderate 1 0 0 1
SA210352CNMI_90Moderate 1 0 0 1
SA210353CNMI_34_BisModerate 1 0 0 1
SA210354CNMI_39Moderate 1 0 0 1
SA210355CNMI_1Moderate 1 0 0 1
SA210356CNMI_22Moderate 1 0 0 1
SA210357CNMI_5Moderate 1 0 0 1
SA210358CNMI_71Moderate 1 0 0 1
SA210359CNMI_14Moderate 1 0 0 1
SA210360CNMI_95Moderate 1 0 0 1
SA210361CNMI_73Moderate 1 0 0 1
SA210362CNMI_4Moderate 1 0 1 0
SA210363CNMI_28Moderate 1 0 1 1
SA210364CNMI_246Moderate 1 0 1 1
SA210365CNMI_59Moderate 1 1 0 0
SA210366CNMI_31Moderate 1 1 0 0
SA210367CNMI_29Moderate 1 1 0 0
SA210368CNMI_89Moderate 1 1 0 0
SA210369CNMI_45Moderate 1 1 0 1
SA210370CNMI_58Moderate 1 1 0 1
SA210371CNMI_13Moderate 1 1 0 1
SA210372CNMI_91Moderate 1 1 0 1
SA210373CNMI_6Moderate 1 1 0 1
SA210374CNMI_78Moderate 1 1 1 1
SA210375CNMI_72Moderate 1 1 1 1
SA210376HT_5NA NA NA NA NA
SA210377HT_1NA NA NA NA NA
SA210378CNMI_0810NA NA NA NA NA
SA210379HT_2NA NA NA NA NA
SA210380HT_3NA NA NA NA NA
SA210381HT_4NA NA NA NA NA
SA210382HT_26Severe 0 0 0 0
SA210383HT_20Severe 0 0 0 1
SA210384CNMI_54Severe 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.

Combined analysis:

Analysis ID AN003591 AN003592
Analysis type MS MS
Chromatography type Other GC
Chromatography system Agilent 7100 CE 8890
Column silica capillary (100 cm; inner diameter, 50 µm, 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, 50 µm, Agilent Technologies)
Chromatography Type:Other
  
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
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