Summary of Study ST003103

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 PR001926. The data can be accessed directly via it's Project DOI: 10.21228/M8RT5W This work is supported by NIH grant, U2C- DK119886.

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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 IDST003103
Study TitleReinforcing the Evidence of Mitochondrial Dysfunction in Long COVID Patients using a Multiplatform Mass Spectrometry-based Metabolomics Approach
Study SummaryDespite the recent and increasing knowledge surrounding COVID-19 infection, the underlying mechanisms of the persistence of symptoms long time after the acute infection are still not completely understood. Here, a multiplatform mass spectrometry-based approach was used for metabolomic and lipidomic profiling of human plasma samples from Long COVID patients (n=40) to reveal mitochondrial dysfunction when compared with individuals fully recovered from acute mild COVID-19 (n=40). Untargeted metabolomic analysis using CE-ESI(+/–)-TOF-MS and GC-Q-MS was performed. Additionally, a lipidomic analysis using LC-ESI(+/–)-QTOF-MS based on an in-house library revealed 471 lipid species identified with high confidence annotation level. The integration of complementary analytical platforms has allowed a comprehensive metabolic and lipidomic characterization of plasma alterations in Long COVID disease that found 46 relevant metabolites which allowed to discriminate between Long COVID and fully recovered patients. We report specific metabolites altered in Long COVID, mainly related to a decrease in the amino acid metabolism and ceramide plasma levels, and an increase in the tricarboxylic acid (TCA) cycle, reinforcing the evidence of an impaired mitochondrial function. The most relevant alterations shown in this study will help to better understand the insights of Long COVID syndrome by providing a deeper knowledge of the metabolomic basis of the pathology.
Institute
Universidad CEU San Pablo
DepartmentChemistry and Biochemistry
LaboratoryCEMBIO
Last NameMartinez
First NameSara
AddressUrbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
Emailsara.martinezlopez@ceu.es
Phone(+34)913724769
Submit Date2024-02-15
Num Groups2
Total Subjects80
Num Males14
Num Females66
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailGC/LC-MS
Release Date2024-03-25
Release Version1
Sara Martinez Sara Martinez
https://dx.doi.org/10.21228/M8RT5W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001926
Project DOI:doi: 10.21228/M8RT5W
Project Title:Reinforcing the Evidence of Mitochondrial Dysfunction in Long COVID Patients using a Multiplatform Mass Spectrometry-based Metabolomics Approach
Project Summary:Despite the recent and increasing knowledge surrounding COVID-19 infection, the underlying mechanisms of the persistence of symptoms long time after the acute infection are still not completely understood. Here, a multiplatform mass spectrometry-based approach was used for metabolomic and lipidomic profiling of human plasma samples from Long COVID patients (n=40) to reveal mitochondrial dysfunction when compared with individuals fully recovered from acute mild COVID-19 (n=40). Untargeted metabolomic analysis using CE-ESI(+/–)-TOF-MS and GC-Q-MS was performed. Additionally, a lipidomic analysis using LC-ESI(+/–)-QTOF-MS based on an in-house library revealed 471 lipid species identified with high confidence annotation level. The integration of complementary analytical platforms has allowed a comprehensive metabolic and lipidomic characterization of plasma alterations in Long COVID disease that found 46 relevant metabolites which allowed to discriminate between Long COVID and fully recovered patients. We report specific metabolites altered in Long COVID, mainly related to a decrease in the amino acid metabolism and ceramide plasma levels, and an increase in the tricarboxylic acid (TCA) cycle, reinforcing the evidence of an impaired mitochondrial function. The most relevant alterations shown in this study will help to better understand the insights of Long COVID syndrome by providing a deeper knowledge of the metabolomic basis of the pathology.
Institute:Universidad CEU San Pablo
Department:Chemistry and Biochemistry
Laboratory:CEMBIO
Last Name:Martinez
First Name:Sara
Address:Urbanización Montepríncipe, Boadilla del Monte, Madrid, 28660, Spain
Email:sara.martinezlopez@ceu.es
Phone:(+34)913724769

Subject:

Subject ID:SU003218
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 Sample source Factor
SA333503L52Plasma Long COVID
SA333504L51Plasma Long COVID
SA333505L50Plasma Long COVID
SA333506L54Plasma Long COVID
SA333507L56Plasma Long COVID
SA333508L58Plasma Long COVID
SA333509L57Plasma Long COVID
SA333510L49Plasma Long COVID
SA333511L55Plasma Long COVID
SA333512L47Plasma Long COVID
SA333513L103Plasma Long COVID
SA333514L102Plasma Long COVID
SA333515L101Plasma Long COVID
SA333516L42Plasma Long COVID
SA333517L43Plasma Long COVID
SA333518L59Plasma Long COVID
SA333519L46Plasma Long COVID
SA333520L45Plasma Long COVID
SA333521L48Plasma Long COVID
SA333522L61Plasma Long COVID
SA333523L74Plasma Long COVID
SA333524L73Plasma Long COVID
SA333525L72Plasma Long COVID
SA333526L75Plasma Long COVID
SA333527L76Plasma Long COVID
SA333528L79Plasma Long COVID
SA333529L78Plasma Long COVID
SA333530L77Plasma Long COVID
SA333531L70Plasma Long COVID
SA333532L69Plasma Long COVID
SA333533L63Plasma Long COVID
SA333534L62Plasma Long COVID
SA333535L100Plasma Long COVID
SA333536L64Plasma Long COVID
SA333537L65Plasma Long COVID
SA333538L68Plasma Long COVID
SA333539L67Plasma Long COVID
SA333540L66Plasma Long COVID
SA333541L60Plasma Long COVID
SA333542L44Plasma Long COVID
SA333543QC2Plasma Quality control
SA333544QC3Plasma Quality control
SA333545QC12Plasma Quality control
SA333546QC11Plasma Quality control
SA333547QC1Plasma Quality control
SA333548QC4Plasma Quality control
SA333549QC10Plasma Quality control
SA333550QC5Plasma Quality control
SA333551QC9Plasma Quality control
SA333552QC8Plasma Quality control
SA333553QC6Plasma Quality control
SA333554QC7Plasma Quality control
SA333555C18Plasma Recovered from acute COVID-19
SA333556C17Plasma Recovered from acute COVID-19
SA333557C19Plasma Recovered from acute COVID-19
SA333558C21Plasma Recovered from acute COVID-19
SA333559C16Plasma Recovered from acute COVID-19
SA333560C20Plasma Recovered from acute COVID-19
SA333561C2Plasma Recovered from acute COVID-19
SA333562C13Plasma Recovered from acute COVID-19
SA333563C10Plasma Recovered from acute COVID-19
SA333564C22Plasma Recovered from acute COVID-19
SA333565C11Plasma Recovered from acute COVID-19
SA333566C12Plasma Recovered from acute COVID-19
SA333567C14Plasma Recovered from acute COVID-19
SA333568C15Plasma Recovered from acute COVID-19
SA333569C23Plasma Recovered from acute COVID-19
SA333570C52Plasma Recovered from acute COVID-19
SA333571C55Plasma Recovered from acute COVID-19
SA333572C49Plasma Recovered from acute COVID-19
SA333573C43Plasma Recovered from acute COVID-19
SA333574C42Plasma Recovered from acute COVID-19
SA333575C59Plasma Recovered from acute COVID-19
SA333576C1Plasma Recovered from acute COVID-19
SA333577C8Plasma Recovered from acute COVID-19
SA333578C7Plasma Recovered from acute COVID-19
SA333579C68Plasma Recovered from acute COVID-19
SA333580C61Plasma Recovered from acute COVID-19
SA333581C41Plasma Recovered from acute COVID-19
SA333582C4Plasma Recovered from acute COVID-19
SA333583C27Plasma Recovered from acute COVID-19
SA333584C29Plasma Recovered from acute COVID-19
SA333585C26Plasma Recovered from acute COVID-19
SA333586C25Plasma Recovered from acute COVID-19
SA333587C24Plasma Recovered from acute COVID-19
SA333588C31Plasma Recovered from acute COVID-19
SA333589C32Plasma Recovered from acute COVID-19
SA333590C37Plasma Recovered from acute COVID-19
SA333591C35Plasma Recovered from acute COVID-19
SA333592C34Plasma Recovered from acute COVID-19
SA333593C33Plasma Recovered from acute COVID-19
SA333594C9Plasma Recovered from acute COVID-19
Showing results 1 to 92 of 92

Collection:

Collection ID:CO003211
Collection Summary:Samples were collected after fasting conditions. 1,500 μL of cold MeOH/EtOH (1:1, v/v) were added to 500 μL of plasma for virus inactivation. Afterward, samples were vigorously mixed using vortex for 1 min, followed by incubation on ice for 5 min, and subsequent centrifugation at 16,000 x g for 20 min at 4 °C to eliminate proteins by precipitation. The resulting extract, containing the metabolites of interest, was transferred to EppendorfTM tubes, and stored at –80 °C until analysis.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003227
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP003224
Sampleprep Summary:For CE-MS analysis 200 µL of frozen plasma extract (MeOH/EtOH 1:1, v/v) were thawed on ice and dried completely using a SpeedVac Concentrator System. The resulting residue was then reconstituted in 100 µL of 0.2 mM MetS dissolved in 0.1 M FA. After vortex-mixing for 1 min, the samples were transferred to a Millipore filter with a 30 kDa protein cutoff and centrifuged at 2,000 x g for 40 min at 4 °C. Finally, the resulting ultrafiltrate was transferred to a CE-MS vial for further analysis. Prior to the analysis vials were centrifuged at 2,000 x g for 10 min at 4 °C to ensure that any possible sediment remained at the bottom of the vial. For GC-MS analysis 200 µL of each plasma extract was thawed on ice to room temperature and 30 µL of the internal standard (IS), palmitic acid-d31 in MeOH (80 mg/mL) was added to it. The mixture was vortexed for 5 min and 200 µL of the solution were transferred to a GC-MS vial. Then, samples were evaporated to dryness using a SpeedVac Concentrator System and maintained at 8 °C in the Gerstel Multiple Purpose Sample (MPS) Preparation Station. An automated two step derivatization process was performed before sample injection using a protocol adjusted from a previous reported method. First, each precipitate was redissolved in 20 µL of O-methoxyamine solution (15 mg/mL in pyridine) for the methoximation process, mixed 10 min at 1,000 rpm and incubated for 90 min at 60 °C at 750 rpm. Second, and after waiting 5 min, 40 µL of BSTFA with 1% TMCS were added for the silylation process. Then, samples were mixed for 10 min at 1,000 rpm and incubated for 60 min at 60 °C at 750 rpm. After waiting 30 min at 8 °C, 80 µL of heptane containing 20 mg/mL of tricosane (IS) were added and mixed for 5 min at 1,000 rpm. Finally, samples were maintained at 8 °C for 30 min before injection. For LC-MS 200 µL of each plasma extract was thawed on ice to room temperature and centrifuged for 10 min at 16,100 x g at 4 °C, transferred to a LC-MS vial and directly injected into the system.

Combined analysis:

Analysis ID AN005077 AN005078 AN005079 AN005080 AN005081
Analysis type MS MS MS MS MS
Chromatography type Reversed phase Reversed phase GC CE CE
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 8890 GC System Agilent 7100 CE Agilent 7100 CE
Column Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) GC DB5-MS column (40 m length, 0.25 mm inner diameter, and 0.25 µm film of 95% dimethyl/5% diphenylpolysiloxane) Agilent Technologies fused silica capillary (total length, 100 cm; internal diameter, 50 µm) Agilent Technologies fused silica capillary (total length, 100 cm; internal diameter, 50 µm)
MS Type ESI ESI EI ESI ESI
MS instrument type QTOF QTOF Single quadrupole TOF TOF
MS instrument name Agilent 6545 QTOF Agilent 6545 QTOF Agilent 5977B Agilent 6230 TOF Agilent 6230 TOF
Ion Mode POSITIVE NEGATIVE UNSPECIFIED POSITIVE NEGATIVE
Units Area Corrected areas Corrected areas Corrected areas Corrected areas

Chromatography:

Chromatography ID:CH003834
Chromatography Summary:RP-UHPLC-ESI(+)-QTOF-MS
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:50°C
Flow Gradient:The chromatographic gradient started at 70 % of B at 0 - 1 min, 86 % B at 3.5 - 10 min, 100% B at 11 - 17 min. The starting conditions were recovered by min 17, followed by a 2 min re-equilibration time, reaching a total running time of 19 min
Flow Rate:0.6 mL/min
Solvent A:10 mM CH3COONH4 and 0.2 mM NH4F in H2O/MeOH (9:1, v/v)
Solvent B:10 mM CH3COONH4 and 0.2 mM NH4F in ACN/MeOH/IPA (2:3:5, v/v/v)
Analytical Time:19 min
Chromatography Type:Reversed phase
  
Chromatography ID:CH003835
Chromatography Summary:RP-UHPLC-ESI(-)-QTOF-MS
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um)
Column Temperature:50°C
Flow Gradient:The chromatographic gradient started at 70 % of B at 0 - 1 min, 86 % B at 3.5 - 10 min, 100% B at 11 - 17 min. The starting conditions were recovered by min 17, followed by a 2 min re-equilibration time, reaching a total running time of 19 min
Flow Rate:0.6 mL/min
Solvent A:10 mM CH3COONH4 and 0.2 mM NH4F in H2O/MeOH (9:1, v/v)
Solvent B:10 mM CH3COONH4 and 0.2 mM NH4F in ACN/MeOH/IPA (2:3:5, v/v/v)
Analytical Time:19 min
Chromatography Type:Reversed phase
  
Chromatography ID:CH003836
Chromatography Summary:GC-Q-MS
Instrument Name:Agilent 8890 GC System
Column Name:GC DB5-MS column (40 m length, 0.25 mm inner diameter, and 0.25 µm film of 95% dimethyl/5% diphenylpolysiloxane)
Column Temperature:The column temperature gradient was programmed as follows: it started at 60 °C for 1 min, then increased by 10 °C/min until reaching 325 °C and held at this temperature for 10 min before cooling down
Flow Gradient:Constant
Flow Rate:0.5658 mL/min
Solvent A:Helium
Solvent B:N/A
Analytical Time:37 min followed by 5 min of post-run period
Chromatography Type:GC
  
Chromatography ID:CH003837
Chromatography Summary:CE-ESI(+)-TOF-MS
Instrument Name:Agilent 7100 CE
Column Name:Agilent Technologies fused silica capillary (total length, 100 cm; internal diameter, 50 µm)
Column Temperature:20°C
Flow Gradient:N/A
Flow Rate:N/A
Solvent A:BGE (1 M FA in 10% MeOH)
Solvent B:N/A
Analytical Time:26 min
Capillary Voltage:30kV
Sheath Liquid:MeOH: H2O (1:1, v/v) with 1mM FA containing two reference masses (purine: 121.0509 and HP-0922: 922.0098) at a flow rate of 0.6 mL/min (1:100 of split ratio)
Chromatography Type:CE
  
Chromatography ID:CH003838
Chromatography Summary:CE-ESI(-)-TOF-MS
Instrument Name:Agilent 7100 CE
Column Name:Agilent Technologies fused silica capillary (total length, 100 cm; internal diameter, 50 µm)
Column Temperature:20°C
Flow Gradient:N/A
Flow Rate:N/A
Solvent A:BGE (1 M FA in 10% MeOH)
Solvent B:N/A
Analytical Time:40 min
Capillary Voltage:-30kV
Sheath Liquid:MeOH: H2O (1:1, v/v) with 1mM FA containing two reference masses (purine: 121.0509 and HP-0922: 922.0098) at a flow rate of 1.0 mL/min (1:100 of split ratio)
Chromatography Type:CE

MS:

MS ID:MS004815
Analysis ID:AN005077
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The mass spectrometer operated in full scan mode, scanning from m/z 40 - 1700 at a scan rate of 3 spectra/s. During the analysis, a solution containing two reference mass compounds was continuously infused to the system at a flow rate of 1 mL/min to provide mass correction. The reference masses used were m/z 121.0509 (purine detected as [C5H4N4 + H]+) and m/z 922.0098 (HP-0921 detected as [C18H18O6N3P3F24 + H]+) for ESI(+) and m/z 119.0363 (purine detected as [C5H4N4 - H]-) and m/z 1033.9881 (HP-0921 detected as [C18H18O6N3P3F24 + CF3COOH-H]-) for ESI(–). At the end of the analysis, ten iterative-MS/MS runs were performed for both, positive and negative ionization modes using a QC sample. They were operated with a MS and MS/MS scan rates of 3 spectra/s, 3 precursors per cycle, a mass range of m/z 40 - 1700, a narrow (~ 1.3 amu) MS/MS isolation width, and 5000 counts and 0.001 % of MS/MS threshold. The collision energy for the first five iterative-MS/MS runs was set at 20 eV, and the subsequent five runs were performed at 40 eV. To ensure accuracy, reference masses and contaminants detected in blank samples were excluded from the analysis. This prevented thein inclusion in the iterative-MS/MS runs. Data was acquired using MassHunter Workstation Software LC-MS Data Acquisition v B.09.00 (Agilent Technologies, Waldbronn, Germany).
Ion Mode:POSITIVE
  
MS ID:MS004816
Analysis ID:AN005078
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The mass spectrometer operated in full scan mode, scanning from m/z 40 - 1700 at a scan rate of 3 spectra/s. During the analysis, a solution containing two reference mass compounds was continuously infused to the system at a flow rate of 1 mL/min to provide mass correction. The reference masses used were m/z 121.0509 (purine detected as [C5H4N4 + H]+) and m/z 922.0098 (HP-0921 detected as [C18H18O6N3P3F24 + H]+) for ESI(+) and m/z 119.0363 (purine detected as [C5H4N4 - H]-) and m/z 1033.9881 (HP-0921 detected as [C18H18O6N3P3F24 + CF3COOH-H]-) for ESI(–). At the end of the analysis, ten iterative-MS/MS runs were performed for both, positive and negative ionization modes using a QC sample. They were operated with a MS and MS/MS scan rates of 3 spectra/s, 3 precursors per cycle, a mass range of m/z 40 - 1700, a narrow (~ 1.3 amu) MS/MS isolation width, and 5000 counts and 0.001 % of MS/MS threshold. The collision energy for the first five iterative-MS/MS runs was set at 20 eV, and the subsequent five runs were performed at 40 eV. To ensure accuracy, reference masses and contaminants detected in blank samples were excluded from the analysis. This prevented thein inclusion in the iterative-MS/MS runs. Data was acquired using MassHunter Workstation Software LC-MS Data Acquisition v B.09.00 (Agilent Technologies, Waldbronn, Germany).
Ion Mode:NEGATIVE
  
MS ID:MS004817
Analysis ID:AN005079
Instrument Name:Agilent 5977B
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:For ionization, the EI source was used with the following settings: filament source temperature at 230 °C and electron ionization energy at 70 eV. Mass spectra were collected in a mass range of m/z 50 - 600 at a scan rate of 2 spectra/s. Mass calibration was performed after every injection with internal reference masses m/z 68.9947, 263.9866 and 501.9706. Data acquisition was performed using the Agilent MassHunter Workstation GC-MS Data Acquisition v 10.0 (Agilent Technologies, Waldbronn, Germany).
Ion Mode:UNSPECIFIED
  
MS ID:MS004818
Analysis ID:AN005080
Instrument Name:Agilent 6230 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:The mass spectra data were acquired in positive polarity mode with a full scan range of m/z 70 - 1000 at a rate of 1.36 spectra/s. The following MS parameters were employed: fragmentor set to 125 V, skimmer to 65 V, OCT RF Vpp to 750 V, drying gas temperature to 200 °C ESI(+), flow rate to 10 L/min, nebulizer to 10 psi, and capillary voltage to 3500 V ESI(+). The Agilent MassHunter Workstation v B.09.00 (Agilent Technologies, Waldbronn, Germany) was used for CE-MS data acquisition.
Ion Mode:POSITIVE
  
MS ID:MS004819
Analysis ID:AN005081
Instrument Name:Agilent 6230 TOF
Instrument Type:TOF
MS Type:ESI
MS Comments:The mass spectra data were acquired in negative polarity mode with a full scan range m/z 60 - 1000 at a rate of 1 spectra/s. The following MS parameters were employed: fragmentor set to 125 V, skimmer to 65 V, OCT RF Vpp to 750 V, drying gas temperature to 275 °C ESI(–), flow rate to 10 L/min, nebulizer to 10 psi, and capillary voltage to 2000 V ESI(-). The Agilent MassHunter Workstation v B.09.00 (Agilent Technologies, Waldbronn, Germany) was used for CE-MS data acquisition.
Ion Mode:NEGATIVE
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