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.

Study ID	ST002404
Study Title	Profiling Metabolites and Lipoproteins in COMETA, an Italian Cohort of COVID-19 patients-part 2
Study Summary	Here, 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 Name	Ghini
First Name	Veronica
Address	via Luigi Sacconi, 6, Sesto Fiorentino, Firenze, 50019, Italy
Email	ghini@cerm.unifi.it
Phone	+390554574266
Submit Date	2022-11-09
Num Groups	2
Total Subjects	605
Num Males	339
Num Females	266
Raw Data Available	Yes
Raw Data File Type(s)	fid
Analysis Type Detail	NMR
Release Date	2023-11-09
Release Version	1

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
SA240144	P_746	F \| Variant:o \| Group:COVID-19_positive \| Severity:mild
SA240145	P_723	F \| Variant:o \| Group:COVID-19_positive \| Severity:mild
SA240146	P_730	F \| Variant:o \| Group:COVID-19_positive \| Severity:mild
SA240147	P_725	F \| Variant:o \| Group:COVID-19_positive \| Severity:mild
SA240148	P_744	F \| Variant:o \| Group:COVID-19_positive \| Severity:mild
SA240149	P_728	F \| Variant:o \| Group:COVID-19_positive \| Severity:mild
SA240150	P_716	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240151	P_721	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240152	P_739	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240153	P_740	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240154	P_738	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240155	P_747	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240156	P_705	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240157	P_708	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240158	P_745	F \| Variant:o \| Group:COVID-19_positive \| Severity:severe
SA240159	P_365	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240160	P_393	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240161	P_232	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240162	P_500	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240163	P_395	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240164	P_388	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240165	P_485	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240166	P_499	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240167	P_234	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240168	P_391	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240169	P_483	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240170	P_479	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240171	P_408	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240172	P_206	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240173	P_207	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240174	P_475	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240175	P_410	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240176	P_416	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240177	P_468	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240178	P_405	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240179	P_210	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240180	P_225	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240181	P_399	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240182	P_217	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240183	P_216	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240184	P_211	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240185	P_215	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240186	P_398	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240187	P_504	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240188	P_318	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240189	P_546	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240190	P_544	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240191	P_347	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240192	P_556	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240193	P_558	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240194	P_349	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240195	P_323	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240196	P_324	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240197	P_533	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240198	P_335	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240199	P_333	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240200	P_534	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240201	P_526	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240202	P_527	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240203	P_303	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240204	P_297	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240205	P_507	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240206	P_271	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240207	P_359	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240208	P_266	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240209	P_362	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240210	P_503	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240211	P_260	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240212	P_358	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240213	P_513	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240214	P_576	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240215	P_571	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240216	P_286	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240217	P_283	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240218	P_589	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240219	P_580	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240220	P_502	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240221	P_402	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240222	P_110	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240223	P_025	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240224	P_428	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240225	P_111	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240226	P_112	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240227	P_426	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240228	P_022	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240229	P_113	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240230	P_098	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240231	P_096	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240232	P_433	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240233	P_064	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240234	P_461	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240235	P_460	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240236	P_459	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240237	P_039	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240238	P_453	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240239	P_021	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240240	P_024	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240241	P_013	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240242	P_010	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity:mild
SA240243	P_467	F \| Variant:wt-α-β \| Group:COVID-19_positive \| Severity: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.

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