Summary of Study ST002404

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 PR001326. The data can be accessed directly via it's Project DOI: 10.21228/M89T2Q 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 IDST002404
Study TitleProfiling Metabolites and Lipoproteins in COMETA, an Italian Cohort of COVID-19 patients-part 2
Study SummaryHere, we report a detailed and comprehensive characterization of the metabolomic and lipoproteomic fingerprint of plasma samples of a high number of hospitalized COVID-19 patients, with different disease severities, infected with different viral variants and with different vaccination statues. Our data deeply extend a first metabolomic/lipoproteomic characterization of the disease published at the beginning of 2022(Ghini V. et al., Plos Path 2022, 18(4):e1010443) performed on a much small number of subjects of the same cohort, infected before a significant spread of the Delta variant and before the administration of the vaccines.
Institute
University of Florence
Last NameGhini
First NameVeronica
Addressvia Luigi Sacconi, 6, Sesto Fiorentino, Firenze, 50019, Italy
Emailghini@cerm.unifi.it
Phone+390554574266
Submit Date2022-11-09
Num Groups2
Total Subjects605
Num Males339
Num Females266
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2023-11-09
Release Version1
Veronica Ghini Veronica Ghini
https://dx.doi.org/10.21228/M89T2Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001326
Project DOI:doi: 10.21228/M89T2Q
Project Title:Profiling metabolites and lipoproteins in COMETA, an Italian cohort of COVID-19 patients
Project Type:NMR-based metabolomics
Project Summary:1H NMR spectra of EDTA-plasma from 246 COVID-19-positive subjects in the acute phase of infection were compared to those of 95 COVID-19-recovered subjects. The two cohorts are largely different (discrimination accuracy > 93%) due to a pool of 16 metabolites and 74 lipoprotein parameters significantly up- or down-regulated in the patients and within the healthy range in the recovered subjects. In 28 post-acute COVID-19-positive patients, the metabolites levels are reverted back to normality whereas the lipoprotein parameters are still altered. Therefore, the metabolite biomarkers might be used as the timeliest sign of the individual response to treatment or spontaneous healing.
Institute:University of Florence
Department:Department of Chemistry
Laboratory:Metabolomics
Last Name:Ghini
First Name:Veronica
Address:via Luigi Sacconi 6
Email:ghini@cerm.unifi.it
Phone:+390554574266
Funding Source:COMETA project, funded by the Tuscany Region,Italy

Subject:

Subject ID:SU002493
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:18-99
Gender:Male and female
Human Inclusion Criteria:Hospitalized COVID-19 patients

Factors:

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

mb_sample_id local_sample_id Sex Variant Group Severity
SA240144P_746F o COVID-19_positive mild
SA240145P_723F o COVID-19_positive mild
SA240146P_730F o COVID-19_positive mild
SA240147P_725F o COVID-19_positive mild
SA240148P_744F o COVID-19_positive mild
SA240149P_728F o COVID-19_positive mild
SA240150P_716F o COVID-19_positive severe
SA240151P_721F o COVID-19_positive severe
SA240152P_739F o COVID-19_positive severe
SA240153P_740F o COVID-19_positive severe
SA240154P_738F o COVID-19_positive severe
SA240155P_747F o COVID-19_positive severe
SA240156P_705F o COVID-19_positive severe
SA240157P_708F o COVID-19_positive severe
SA240158P_745F o COVID-19_positive severe
SA240159P_365F wt-α-β COVID-19_positive mild
SA240160P_393F wt-α-β COVID-19_positive mild
SA240161P_232F wt-α-β COVID-19_positive mild
SA240162P_500F wt-α-β COVID-19_positive mild
SA240163P_395F wt-α-β COVID-19_positive mild
SA240164P_388F wt-α-β COVID-19_positive mild
SA240165P_485F wt-α-β COVID-19_positive mild
SA240166P_499F wt-α-β COVID-19_positive mild
SA240167P_234F wt-α-β COVID-19_positive mild
SA240168P_391F wt-α-β COVID-19_positive mild
SA240169P_483F wt-α-β COVID-19_positive mild
SA240170P_479F wt-α-β COVID-19_positive mild
SA240171P_408F wt-α-β COVID-19_positive mild
SA240172P_206F wt-α-β COVID-19_positive mild
SA240173P_207F wt-α-β COVID-19_positive mild
SA240174P_475F wt-α-β COVID-19_positive mild
SA240175P_410F wt-α-β COVID-19_positive mild
SA240176P_416F wt-α-β COVID-19_positive mild
SA240177P_468F wt-α-β COVID-19_positive mild
SA240178P_405F wt-α-β COVID-19_positive mild
SA240179P_210F wt-α-β COVID-19_positive mild
SA240180P_225F wt-α-β COVID-19_positive mild
SA240181P_399F wt-α-β COVID-19_positive mild
SA240182P_217F wt-α-β COVID-19_positive mild
SA240183P_216F wt-α-β COVID-19_positive mild
SA240184P_211F wt-α-β COVID-19_positive mild
SA240185P_215F wt-α-β COVID-19_positive mild
SA240186P_398F wt-α-β COVID-19_positive mild
SA240187P_504F wt-α-β COVID-19_positive mild
SA240188P_318F wt-α-β COVID-19_positive mild
SA240189P_546F wt-α-β COVID-19_positive mild
SA240190P_544F wt-α-β COVID-19_positive mild
SA240191P_347F wt-α-β COVID-19_positive mild
SA240192P_556F wt-α-β COVID-19_positive mild
SA240193P_558F wt-α-β COVID-19_positive mild
SA240194P_349F wt-α-β COVID-19_positive mild
SA240195P_323F wt-α-β COVID-19_positive mild
SA240196P_324F wt-α-β COVID-19_positive mild
SA240197P_533F wt-α-β COVID-19_positive mild
SA240198P_335F wt-α-β COVID-19_positive mild
SA240199P_333F wt-α-β COVID-19_positive mild
SA240200P_534F wt-α-β COVID-19_positive mild
SA240201P_526F wt-α-β COVID-19_positive mild
SA240202P_527F wt-α-β COVID-19_positive mild
SA240203P_303F wt-α-β COVID-19_positive mild
SA240204P_297F wt-α-β COVID-19_positive mild
SA240205P_507F wt-α-β COVID-19_positive mild
SA240206P_271F wt-α-β COVID-19_positive mild
SA240207P_359F wt-α-β COVID-19_positive mild
SA240208P_266F wt-α-β COVID-19_positive mild
SA240209P_362F wt-α-β COVID-19_positive mild
SA240210P_503F wt-α-β COVID-19_positive mild
SA240211P_260F wt-α-β COVID-19_positive mild
SA240212P_358F wt-α-β COVID-19_positive mild
SA240213P_513F wt-α-β COVID-19_positive mild
SA240214P_576F wt-α-β COVID-19_positive mild
SA240215P_571F wt-α-β COVID-19_positive mild
SA240216P_286F wt-α-β COVID-19_positive mild
SA240217P_283F wt-α-β COVID-19_positive mild
SA240218P_589F wt-α-β COVID-19_positive mild
SA240219P_580F wt-α-β COVID-19_positive mild
SA240220P_502F wt-α-β COVID-19_positive mild
SA240221P_402F wt-α-β COVID-19_positive mild
SA240222P_110F wt-α-β COVID-19_positive mild
SA240223P_025F wt-α-β COVID-19_positive mild
SA240224P_428F wt-α-β COVID-19_positive mild
SA240225P_111F wt-α-β COVID-19_positive mild
SA240226P_112F wt-α-β COVID-19_positive mild
SA240227P_426F wt-α-β COVID-19_positive mild
SA240228P_022F wt-α-β COVID-19_positive mild
SA240229P_113F wt-α-β COVID-19_positive mild
SA240230P_098F wt-α-β COVID-19_positive mild
SA240231P_096F wt-α-β COVID-19_positive mild
SA240232P_433F wt-α-β COVID-19_positive mild
SA240233P_064F wt-α-β COVID-19_positive mild
SA240234P_461F wt-α-β COVID-19_positive mild
SA240235P_460F wt-α-β COVID-19_positive mild
SA240236P_459F wt-α-β COVID-19_positive mild
SA240237P_039F wt-α-β COVID-19_positive mild
SA240238P_453F wt-α-β COVID-19_positive mild
SA240239P_021F wt-α-β COVID-19_positive mild
SA240240P_024F wt-α-β COVID-19_positive mild
SA240241P_013F wt-α-β COVID-19_positive mild
SA240242P_010F wt-α-β COVID-19_positive mild
SA240243P_467F wt-α-β COVID-19_positive mild
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Collection:

Collection ID:CO002486
Collection Summary:The analysed were done on EDTA-plasma. All the samples were collected, processed and stored following the ISO standards (ISO 23118:2021), designed for high quality biological samples for metabolomic analysis.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002505
Treatment Summary:Not Applicable

Sample Preparation:

Sampleprep ID:SP002499
Sampleprep Summary:Frozen EDTA-plasma samples were thawed at room temperature and shaken before use. A total of 350 μL of sodium phosphate buffer (70 mM Na2HPO4; 20% (v/v) 2H2O; 6.1 mM NaN3, 4.6 mM sodium trimethylsilyl [2,2,3,3−2H4] propionate (TMSP), pH 7.4) was added to 350 μL of each serum sample; the mixture was homogenized by vortexing for 30 s. A total of 600 μL of each mixture was transferred into a 5.00 mm NMR tube (Bruker BioSpin) for the analysis.

Analysis:

Analysis ID:AN003918
Analysis Type:NMR
Num Factors:16
Num Metabolites:139
Units:Relative abundance

NMR:

NMR ID:NM000258
Analysis ID:AN003918
Instrument Name:Bruker 600 MHz
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Spectrometer Frequency:600 MHz
NMR Probe:5-mm PATXI 1H-13C-15N and 2H-decoupling probe
NMR Solvent:H2O
NMR Tube Size:5 mm
Pulse Sequence:noesygp1D
Water Suppression:water peak suppression-presaturation
Receiver Gain:90.5
Temperature:310 K
Number Of Scans:32
Dummy Scans:4
Acquisition Time:2.7s
Relaxation Delay:4s
Spectral Width:18,028 Hz
Num Data Points Acquired:98000
Line Broadening:0.3
Baseline Correction Method:automatic
Chemical Shift Ref Std:doublet at 5.24 ppm
Binned Increment:0.02 ppm
Binned Data Excluded Range:4.5-5.5 ppm
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