{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002087","ANALYSIS_ID":"AN003405","VERSION":"1","CREATED_ON":"February 22, 2022, 1:04 am"}, "PROJECT":{"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"}, "STUDY":{"STUDY_TITLE":"Profiling metabolites and lipoproteins in COMETA, an Italian cohort of COVID-19 patients","STUDY_TYPE":"NMR-based metabolomics","STUDY_SUMMARY":"1H NMR spectra of EDTA-plasma from 246 COVID-19-positive subjects in the acute phase of infection were compared to those of 94 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","EMAIL":"ghini@cerm.unifi.it","PHONE":"+390554574266","NUM_GROUPS":"3","TOTAL_SUBJECTS":"368","NUM_MALES":"201","NUM_FEMALES":"167"}, "SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Male and female","HUMAN_INCLUSION_CRITERIA":"hospedalized COVID-19 patients"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"6", "Sample ID":"6", "Factors":{"Grade of severity":"Asymptomatic","Group":"COVID-19<21days"}, "Additional sample data":{"RAW_FILE_NAME":"6","SEX":"male","AGE":"72"} }, { "Subject ID":"7", "Sample ID":"7", "Factors":{"Grade of severity":"Asymptomatic","Group":"COVID-19<21days"}, "Additional sample 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{ "Subject ID":"186", "Sample ID":"186", "Factors":{"Grade of severity":"Asymptomatic","Group":"Post-COVID-27"}, "Additional sample data":{"RAW_FILE_NAME":"186","SEX":"female","AGE":"50"} }, { "Subject ID":"187", "Sample ID":"187", "Factors":{"Grade of severity":"Asymptomatic","Group":"Post-COVID-28"}, "Additional sample data":{"RAW_FILE_NAME":"187","SEX":"male","AGE":"66"} }, { "Subject ID":"192", "Sample ID":"192", "Factors":{"Grade of severity":"Asymptomatic","Group":"Post-COVID-29"}, "Additional sample data":{"RAW_FILE_NAME":"192","SEX":"female","AGE":"35"} }, { "Subject ID":"346", "Sample ID":"346", "Factors":{"Grade of severity":"Asymptomatic","Group":"Post-COVID-30"}, "Additional sample data":{"RAW_FILE_NAME":"346","SEX":"male","AGE":"64"} }, { "Subject ID":"382", "Sample ID":"382", "Factors":{"Grade of severity":"Asymptomatic","Group":"Post-COVID-31"}, "Additional sample data":{"RAW_FILE_NAME":"382","SEX":"male","AGE":"71"} }, { "Subject ID":"4", "Sample ID":"4", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-32"}, "Additional sample data":{"RAW_FILE_NAME":"4","SEX":"female","AGE":"93"} }, { "Subject ID":"51", "Sample ID":"51", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-33"}, "Additional sample data":{"RAW_FILE_NAME":"51","SEX":"male","AGE":"37"} }, { "Subject ID":"58", "Sample ID":"58", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-34"}, "Additional sample data":{"RAW_FILE_NAME":"58","SEX":"male","AGE":"59"} }, { "Subject ID":"59", "Sample ID":"59", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-35"}, "Additional sample data":{"RAW_FILE_NAME":"59","SEX":"male","AGE":"64"} }, { "Subject ID":"60", "Sample ID":"60", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-36"}, "Additional sample data":{"RAW_FILE_NAME":"60","SEX":"female","AGE":"57"} }, { "Subject ID":"67", "Sample ID":"67", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-37"}, "Additional sample 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"Factors":{"Grade of severity":"Mild","Group":"Post-COVID-43"}, "Additional sample data":{"RAW_FILE_NAME":"106","SEX":"male","AGE":"72"} }, { "Subject ID":"108", "Sample ID":"108", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-44"}, "Additional sample data":{"RAW_FILE_NAME":"108","SEX":"female","AGE":"89"} }, { "Subject ID":"124", "Sample ID":"124", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-45"}, "Additional sample data":{"RAW_FILE_NAME":"124","SEX":"male","AGE":"71"} }, { "Subject ID":"125", "Sample ID":"125", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-46"}, "Additional sample data":{"RAW_FILE_NAME":"125","SEX":"female","AGE":"55"} }, { "Subject ID":"161", "Sample ID":"161", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-47"}, "Additional sample data":{"RAW_FILE_NAME":"161","SEX":"female","AGE":"61"} }, { "Subject ID":"162", "Sample ID":"162", "Factors":{"Grade of severity":"Mild","Group":"Post-COVID-48"}, "Additional sample 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"Additional sample data":{"RAW_FILE_NAME":"45","SEX":"male","AGE":"63"} }, { "Subject ID":"46", "Sample ID":"46", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-60"}, "Additional sample data":{"RAW_FILE_NAME":"46","SEX":"male","AGE":"68"} }, { "Subject ID":"47", "Sample ID":"47", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-61"}, "Additional sample data":{"RAW_FILE_NAME":"47","SEX":"male","AGE":"65"} }, { "Subject ID":"48", "Sample ID":"48", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-62"}, "Additional sample data":{"RAW_FILE_NAME":"48","SEX":"female","AGE":"64"} }, { "Subject ID":"57", "Sample ID":"57", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-63"}, "Additional sample data":{"RAW_FILE_NAME":"57","SEX":"female","AGE":"66"} }, { "Subject ID":"81", "Sample ID":"81", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-64"}, "Additional sample data":{"RAW_FILE_NAME":"81","SEX":"female","AGE":"74"} }, { "Subject ID":"88", "Sample ID":"88", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-65"}, "Additional sample data":{"RAW_FILE_NAME":"88","SEX":"female","AGE":"71"} }, { "Subject ID":"105", "Sample ID":"105", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-66"}, "Additional sample data":{"RAW_FILE_NAME":"105","SEX":"male","AGE":"58"} }, { "Subject ID":"118", "Sample ID":"118", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-67"}, "Additional sample data":{"RAW_FILE_NAME":"118","SEX":"female","AGE":"59"} }, { "Subject ID":"119", "Sample ID":"119", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-68"}, "Additional sample data":{"RAW_FILE_NAME":"119","SEX":"male","AGE":"81"} }, { "Subject ID":"121", "Sample ID":"121", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-69"}, "Additional sample data":{"RAW_FILE_NAME":"121","SEX":"male","AGE":"78"} }, { "Subject ID":"122", "Sample ID":"122", "Factors":{"Grade of 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severity":"Moderate","Group":"Post-COVID-86"}, "Additional sample data":{"RAW_FILE_NAME":"325","SEX":"male","AGE":"50"} }, { "Subject ID":"326", "Sample ID":"326", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-87"}, "Additional sample data":{"RAW_FILE_NAME":"326","SEX":"male","AGE":"64"} }, { "Subject ID":"328", "Sample ID":"328", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-88"}, "Additional sample data":{"RAW_FILE_NAME":"328","SEX":"female","AGE":"80"} }, { "Subject ID":"329", "Sample ID":"329", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-89"}, "Additional sample data":{"RAW_FILE_NAME":"329","SEX":"female","AGE":"61"} }, { "Subject ID":"342", "Sample ID":"342", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-90"}, "Additional sample data":{"RAW_FILE_NAME":"342","SEX":"male","AGE":"61"} }, { "Subject ID":"343", "Sample ID":"343", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-91"}, "Additional sample 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severity":"Moderate","Group":"Post-COVID-102"}, "Additional sample data":{"RAW_FILE_NAME":"383","SEX":"female","AGE":"82"} }, { "Subject ID":"384", "Sample ID":"384", "Factors":{"Grade of severity":"Moderate","Group":"Post-COVID-103"}, "Additional sample data":{"RAW_FILE_NAME":"384","SEX":"male","AGE":"71"} }, { "Subject ID":"82", "Sample ID":"82", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-104"}, "Additional sample data":{"RAW_FILE_NAME":"82","SEX":"male","AGE":"68"} }, { "Subject ID":"85", "Sample ID":"85", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-105"}, "Additional sample data":{"RAW_FILE_NAME":"85","SEX":"female","AGE":"50"} }, { "Subject ID":"86", "Sample ID":"86", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-106"}, "Additional sample data":{"RAW_FILE_NAME":"86","SEX":"female","AGE":"80"} }, { "Subject ID":"87", "Sample ID":"87", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-107"}, "Additional sample data":{"RAW_FILE_NAME":"87","SEX":"female","AGE":"65"} }, { "Subject ID":"107", "Sample ID":"107", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-108"}, "Additional sample data":{"RAW_FILE_NAME":"107","SEX":"male","AGE":"78"} }, { "Subject ID":"181", "Sample ID":"181", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-109"}, "Additional sample data":{"RAW_FILE_NAME":"181","SEX":"female","AGE":"74"} }, { "Subject ID":"189", "Sample ID":"189", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-110"}, "Additional sample data":{"RAW_FILE_NAME":"189","SEX":"male","AGE":"57"} }, { "Subject ID":"278", "Sample ID":"278", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-111"}, "Additional sample data":{"RAW_FILE_NAME":"278","SEX":"male","AGE":"72"} }, { "Subject ID":"279", "Sample ID":"279", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-112"}, "Additional sample data":{"RAW_FILE_NAME":"279","SEX":"male","AGE":"79"} }, { "Subject ID":"327", "Sample ID":"327", "Factors":{"Grade of severity":"Severe","Group":"Post-COVID-113"}, "Additional sample data":{"RAW_FILE_NAME":"327","SEX":"male","AGE":"53"} } ], "COLLECTION":{"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_SUMMARY":"not applicable"}, "SAMPLEPREP":{"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":{"LABORATORY_NAME":"Metabolomics"}, "NM":{"INSTRUMENT_NAME":"Bruker 600MHZ","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_TUBE_SIZE":"5 mm","PULSE_SEQUENCE":"noesygp1d","WATER_SUPPRESSION":"water peak suppression","DUMMY_SCANS":"4","ACQUISITION_TIME":"2.7 s","RELAXATION_DELAY":"4 s","SPECTRAL_WIDTH":"18,028 Hz","NUM_DATA_POINTS_ACQUIRED":"98000","LINE_BROADENING":"0.3","BASELINE_CORRECTION_METHOD":"automatic baseline correction","CHEMICAL_SHIFT_REF_STD":"doublet at 5.24 ppm","BINNED_INCREMENT":"0.2 ppm","BINNED_DATA_EXCLUDED_RANGE":"4.5-5.5 ppm"}, "NMR_METABOLITE_DATA":{ "Units":"uM", 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ID":"na"},{"Metabolite":"FreeCholesterol_LDL4","KEGG ID":"na"},{"Metabolite":"FreeCholesterol_LDL5","KEGG ID":"na"},{"Metabolite":"FreeCholesterol_LDL6","KEGG ID":"na"},{"Metabolite":"Phospholipids_LDL1","KEGG ID":"na"},{"Metabolite":"Phospholipids_LDL2","KEGG ID":"na"},{"Metabolite":"Phospholipids_LDL3","KEGG ID":"na"},{"Metabolite":"Phospholipids_LDL4","KEGG ID":"na"},{"Metabolite":"Phospholipids_LDL5","KEGG ID":"na"},{"Metabolite":"Phospholipids_LDL6","KEGG ID":"na"},{"Metabolite":"ApoB_LDL1","KEGG ID":"na"},{"Metabolite":"ApoB_LDL2","KEGG ID":"na"},{"Metabolite":"ApoB_LDL3","KEGG ID":"na"},{"Metabolite":"ApoB_LDL4","KEGG ID":"na"},{"Metabolite":"ApoB_LDL5","KEGG ID":"na"},{"Metabolite":"ApoB_LDL6","KEGG ID":"na"},{"Metabolite":"Triglycerides_HDL1","KEGG ID":"na"},{"Metabolite":"Triglycerides_HDL2","KEGG ID":"na"},{"Metabolite":"Triglycerides_HDL3","KEGG ID":"na"},{"Metabolite":"Triglycerides_HDL4","KEGG ID":"na"},{"Metabolite":"Cholesterol_HDL1","KEGG ID":"na"},{"Metabolite":"Cholesterol_HDL2","KEGG ID":"na"},{"Metabolite":"Cholesterol_HDL3","KEGG ID":"na"},{"Metabolite":"Cholesterol_HDL4","KEGG ID":"na"},{"Metabolite":"FreeCholesterol_HDL1","KEGG ID":"na"},{"Metabolite":"FreeCholesterol_HDL2","KEGG ID":"na"},{"Metabolite":"FreeCholesterol_HDL3","KEGG ID":"na"},{"Metabolite":"FreeCholesterol_HDL4","KEGG ID":"na"},{"Metabolite":"Phospholipids_HDL1","KEGG ID":"na"},{"Metabolite":"Phospholipids_HDL2","KEGG ID":"na"},{"Metabolite":"Phospholipids_HDL3","KEGG ID":"na"},{"Metabolite":"Phospholipids_HDL4","KEGG ID":"na"},{"Metabolite":"ApoA1_HDL1","KEGG ID":"na"},{"Metabolite":"ApoA1_HDL2","KEGG ID":"na"},{"Metabolite":"ApoA1_HDL3","KEGG ID":"na"},{"Metabolite":"ApoA1_HDL4","KEGG ID":"na"},{"Metabolite":"ApoA2_HDL1","KEGG ID":"na"},{"Metabolite":"ApoA2_HDL2","KEGG ID":"na"},{"Metabolite":"ApoA2_HDL3","KEGG ID":"na"},{"Metabolite":"ApoA2_HDL4","KEGG ID":"na"}] } }