Summary of Study ST002016

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 PR001280. The data can be accessed directly via it's Project DOI: 10.21228/M88715 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 IDST002016
Study TitleMetabolomics of COVID patients
Study TypeUntargeted Metabolomics
Study SummaryUntargeted metabolite analysis was performed on a Thermo Orbitrap IDX Tribrid MS to understand changes in metabolites due to COVID severity.
Institute
University of Virginia
Department1Department of Biochemistry & Molecular Genetics; School of Medicine Core Facilities; Department of Microbiology, Immunology, and Cancer Biology; Department of Biomedical Engineering
LaboratoryBiomolecular Analysis Facility, Univ of Virginia School of Medicine
Last NameWase
First NameNishikant
AddressBiomolecular Analysis Facility, Pinn Hall Room No 1105B
Emailnw5es@virginia.edu
Phone4023109931
Submit Date2021-12-14
Num Groups6
Total Subjects140
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-07-29
Release Version1
Nishikant Wase Nishikant Wase
https://dx.doi.org/10.21228/M88715
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001280
Project DOI:doi: 10.21228/M88715
Project Title:Leveraging Untargeted Metabolomics and Metabolic Modeling to Identify Functional Metabolic Alterations Associated with COVID-19 Disease Severity
Project Type:Untargeted Metabolomics (UPLC-MS/MS)
Project Summary:Untargeted metabolomics of COVID patients
Institute:University of Virginia
Department:Department of Biochemistry & Molecular Genetics; School of Medicine Core Facilities; Department of Microbiology, Immunology, and Cancer Biology; Department of Biomedical Engineering
Laboratory:Biomolecular Analysis Facility, Univ of Virginia School of Medicine
Last Name:Wase
First Name:Nishikant
Address:Biomolecular Analysis Facility
Email:nw5es@virginia.edu
Phone:4023109931

Subject:

Subject ID:SU002097
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 group
SA188663Blank_01_POS-
SA188664Pooled_QC_ID_04_POS-
SA188665Pooled_QC_ID_02_POS-
SA188666Blank_02_NEG-
SA188667Pooled_QC_ID_03_POS-
SA188668Pooled_QC_ID_01_NEG-
SA188669Pooled_QC_ID_04_NEG-
SA188670Pooled_QC_ID_03_NEG-
SA188671Pooled_QC_ID_02_NEG-
SA188672Pooled_QC_ID_01_POS-
SA188673Blank_01_NEG-
SA188674Blank_02_POS-
SA188683Pat_134_POSCOVID_before_ventilator
SA188684Pat_31_NEGCOVID_before_ventilator
SA188685Pat_25_NEGCOVID_before_ventilator
SA188686Pat_21_NEGCOVID_before_ventilator
SA188687Pat_17_NEGCOVID_before_ventilator
SA188688Pat_21_POSCOVID_before_ventilator
SA188689Pat_88_POSCOVID_before_ventilator
SA188690Pat_31_POSCOVID_before_ventilator
SA188691Pat_25_POSCOVID_before_ventilator
SA188692Pat_113_NEGCOVID_before_ventilator
SA188693Pat_17_POSCOVID_before_ventilator
SA188694Pat_134_NEGCOVID_before_ventilator
SA188695Pat_113_POSCOVID_before_ventilator
SA188696Pat_88_NEGCOVID_before_ventilator
SA188675Pat_117_NEGCOVID_ICU-no vent
SA188676Pat_16_POSCOVID_ICU-no vent
SA188677Pat_16_NEGCOVID_ICU-no vent
SA188678Pat_117_POSCOVID_ICU-no vent
SA188679Pat_100_NEGCOVID_ICU-no vent
SA188680Pat_82_POSCOVID_ICU-no vent
SA188681Pat_100_POSCOVID_ICU-no vent
SA188682Pat_82_NEGCOVID_ICU-no vent
SA188697Pat_98_POSCOVID_non-acute
SA188698Pat_99_POSCOVID_non-acute
SA188699Pat_04_POSCOVID_non-acute
SA188700Pat_97_POSCOVID_non-acute
SA188701Pat_96_POSCOVID_non-acute
SA188702Pat_93_POSCOVID_non-acute
SA188703Pat_01_NEGCOVID_non-acute
SA188704Pat_94_POSCOVID_non-acute
SA188705Pat_99_NEGCOVID_non-acute
SA188706Pat_110_NEGCOVID_non-acute
SA188707Pat_97_NEGCOVID_non-acute
SA188708Pat_111_NEGCOVID_non-acute
SA188709Pat_109_NEGCOVID_non-acute
SA188710Pat_106_NEGCOVID_non-acute
SA188711Pat_03_NEGCOVID_non-acute
SA188712Pat_98_NEGCOVID_non-acute
SA188713Pat_101_NEGCOVID_non-acute
SA188714Pat_92_POSCOVID_non-acute
SA188715Pat_91_POSCOVID_non-acute
SA188716Pat_77_POSCOVID_non-acute
SA188717Pat_79_POSCOVID_non-acute
SA188718Pat_80_POSCOVID_non-acute
SA188719Pat_76_POSCOVID_non-acute
SA188720Pat_75_POSCOVID_non-acute
SA188721Pat_72_POSCOVID_non-acute
SA188722Pat_73_POSCOVID_non-acute
SA188723Pat_74_POSCOVID_non-acute
SA188724Pat_81_POSCOVID_non-acute
SA188725Pat_01_POSCOVID_non-acute
SA188726Pat_87_POSCOVID_non-acute
SA188727Pat_03_POSCOVID_non-acute
SA188728Pat_89_POSCOVID_non-acute
SA188729Pat_86_POSCOVID_non-acute
SA188730Pat_85_POSCOVID_non-acute
SA188731Pat_83_POSCOVID_non-acute
SA188732Pat_84_POSCOVID_non-acute
SA188733Pat_96_NEGCOVID_non-acute
SA188734Pat_94_NEGCOVID_non-acute
SA188735Pat_32_NEGCOVID_non-acute
SA188736Pat_71_NEGCOVID_non-acute
SA188737Pat_72_NEGCOVID_non-acute
SA188738Pat_85_NEGCOVID_non-acute
SA188739Pat_28_NEGCOVID_non-acute
SA188740Pat_23_NEGCOVID_non-acute
SA188741Pat_26_NEGCOVID_non-acute
SA188742Pat_27_NEGCOVID_non-acute
SA188743Pat_73_NEGCOVID_non-acute
SA188744Pat_74_NEGCOVID_non-acute
SA188745Pat_80_NEGCOVID_non-acute
SA188746Pat_81_NEGCOVID_non-acute
SA188747Pat_84_NEGCOVID_non-acute
SA188748Pat_79_NEGCOVID_non-acute
SA188749Pat_77_NEGCOVID_non-acute
SA188750Pat_75_NEGCOVID_non-acute
SA188751Pat_76_NEGCOVID_non-acute
SA188752Pat_22_NEGCOVID_non-acute
SA188753Pat_86_NEGCOVID_non-acute
SA188754Pat_130_NEGCOVID_non-acute
SA188755Pat_92_NEGCOVID_non-acute
SA188756Pat_91_NEGCOVID_non-acute
SA188757Pat_123_NEGCOVID_non-acute
SA188758Pat_121_NEGCOVID_non-acute
SA188759Pat_83_NEGCOVID_non-acute
SA188760Pat_93_NEGCOVID_non-acute
SA188761Pat_131_NEGCOVID_non-acute
SA188762Pat_132_NEGCOVID_non-acute
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Collection:

Collection ID:CO002090
Collection Summary:Blood samples were collected in EDTA tubes from 84 adult patients who tested positive by PCR for SARS-CoV2 at the University of Virginia hospital between April and June 2020. Plasma prepared from the blood was stored at -70oC. A total of 48 of the samples were from out-patients and categorized as non-severe COVID-19, while 36 samples were categorized as severe COVID-19 based on the need for hospitalization and in some cases ICU and ventilator requirements (four and 25, respectively)
Sample Type:Blood (plasma)
Collection Method:EDTA Tubes
Storage Conditions:Described in summary

Treatment:

Treatment ID:TR002109
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002103
Sampleprep Summary:plasma samples were thawed on ice and 50 µL of plasma was retained for the metabolome analysis. Approximately 200 µL of cold methanol was added to the plasma sample and shaken vigorously to inactivate any potential viruses. The samples were stored in -80 ºC immediately until extraction for metabolomics experiments. For extraction, 200 µL of cold methanol was added to each tube, vortexed and shaken vigorously for 30 min at 4 ºC in a temperature controlled thermal shaker. Further 200 µL of chloroform and 400 µL of water were added, shaken vigorously and the top aqueous phase was recovered as a metabolite mixture of diverse chemical nature. Each metabolite extract was dried overnight in speedVac and reconstituted in 60 µL of 0.1% formic acid in water. Ten microliters from each tube were removed to create a pooled QC sample that was injected at the beginning and end of the MS sequence run and additional QC samples were injected after every 10 sample injections.
Processing Storage Conditions:Described in summary
Extraction Method:Described above
Extract Storage:Described in summary
Sample Resuspension:0.1% formic acid

Combined analysis:

Analysis ID AN003284 AN003285
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Thermo Accucore C18 (100 x 2.1mm,2.6um) Thermo Accucore C18 (100 x 2.1mm,2.6um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Orbitrap ID-X tribrid Thermo Orbitrap ID-X tribrid
Ion Mode POSITIVE NEGATIVE
Units intensity intensity

Chromatography:

Chromatography ID:CH002425
Chromatography Summary:Samples were injected in randomized fashion via a Thermo Vanquish UHPLC and separation of the polar metabolites was achieved using Thermo Accucore C18 column (Thermo Scientific; 2.1 x 100 mm; 1.5 µm) maintained at 30 °C. The injection volume was 10 µL. For the 15-minute gradient, the standard mobile phase for RPLC was A = 0.1% formic acid in water and B = 0.1% formic acid in methanol. The linear elution gradient was as follows: 0-8.0 minutes at 50% B, 8.0 – 13.0 minutes held at 98% B, 13.1 to 15.0 minutes revert to 0% B to re-equilibration for next injection at a flow rate of 0.25 mL/min.
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore C18 (100 x 2.1mm,2.6um)
Column Temperature:30C
Flow Gradient:0-8 minutes 50% B, 8 - 13 minutes held at 98% B, 13.1 to 15.0 minutes revert to 0% B to re-equilibration for next injection
Flow Rate:0.25 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003055
Analysis ID:AN003284
Instrument Name:Thermo Orbitrap ID-X tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HESI) source was operated at 3.5 kV and 2.5kV for positive and negative modes, respectively. Ion source sheath gas was set at 35 and auxiliary gas at 7. Ion transfer tube temperature was maintained at 275 °C while vaporizer temperature was maintained at 320 °C. The instrument was set to acquire over the m/z range 67-1000, in full MS mode (1 µscan) at a resolution of 60,000 at a normalized AGC Target of 25% and 50 milliseconds of maximum injection time was allowed. RF lens amplitude was set at 35%. Tandem MS/MS performed by applying quadrupole isolation with an isolation window of 1.6 m/z. Activation type was set at HCD and masses were fragmented with HCD Assisted Collision Energy (%) of 15,35,50. Fragment masses were detected by Orbitrap at a resolution of 15,000.
Ion Mode:POSITIVE
  
MS ID:MS003056
Analysis ID:AN003285
Instrument Name:Thermo Orbitrap ID-X tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HESI) source was operated at 3.5 kV and 2.5kV for positive and negative modes, respectively. Ion source sheath gas was set at 35 and auxiliary gas at 7. Ion transfer tube temperature was maintained at 275 °C while vaporizer temperature was maintained at 320 °C. The instrument was set to acquire over the m/z range 67-1000, in full MS mode (1 µscan) at a resolution of 60,000 at a normalized AGC Target of 25% and 50 milliseconds of maximum injection time was allowed. RF lens amplitude was set at 35%. Tandem MS/MS performed by applying quadrupole isolation with an isolation window of 1.6 m/z. Activation type was set at HCD and masses were fragmented with HCD Assisted Collision Energy (%) of 15,35,50. Fragment masses were detected by Orbitrap at a resolution of 15,000.
Ion Mode:NEGATIVE
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