{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002477","ANALYSIS_ID":"AN004046","VERSION":"1","CREATED_ON":"February 15, 2023, 8:15 am"},
"PROJECT":{"PROJECT_TITLE":"Human neutrophil metabolomics","PROJECT_TYPE":"MS qualitative analysis","PROJECT_SUMMARY":"Severe COVID-19 is characterized by an increase in the number and changes in the function of innate immune cells including neutrophils. However, it is not known how the metabolome of immune cells changes in COVID-19 patients or how metabolic changes may contribute to immune dysfunction. To address these questions, we analyzed the metabolome of neutrophils from patients with severe or mild COVID-19, or healthy controls. We identified widespread dysregulation of neutrophil metabolism with disease progression including in amino acid, redox, and central carbon metabolism.","INSTITUTE":"UT Southwestern Medical Center","DEPARTMENT":"Children's Research Institute","LAST_NAME":"Li","FIRST_NAME":"Yafeng","ADDRESS":"5323 Harry Hines Blvd, Children's Research Institute, Dallas, TX, 75309, USA","EMAIL":"yafeng.li@utsouthwestern.edu","PHONE":"4047696693"},
"STUDY":{"STUDY_TITLE":"Neutrophil metabolomics in COVID-19","STUDY_SUMMARY":"Severe COVID-19 is characterized by an increase in the number and changes in the function of innate immune cells including neutrophils. However, it is not known how the metabolome of immune cells changes in COVID-19 patients or how metabolic changes may contribute to immune dysfunction. To address these questions, we analyzed the metabolome of neutrophils from patients with severe or mild COVID-19, or healthy controls. We identified widespread dysregulation of neutrophil metabolism with disease progression including in amino acid, redox, and central carbon metabolism.","INSTITUTE":"UT Southwestern Medical Center","LAST_NAME":"Li","FIRST_NAME":"Yafeng","ADDRESS":"5323 Harry Hines Blvd, Children's Research Institute, Dallas, TX, 75309, USA","EMAIL":"yafeng.li@utsouthwestern.edu","PHONE":"4047696693"},
"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
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"Sample ID":"PMN_66",
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"Sample ID":"PMN_68",
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"Sample ID":"PMN_69",
"Factors":{"Experimental Factors":"Severe"},
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"Sample ID":"PMN_70",
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"Sample ID":"PMN_71",
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"Sample ID":"PMN_73",
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"Sample ID":"PMN_75",
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"Sample ID":"PMN_78",
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"Sample ID":"PMN_79",
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"Sample ID":"PMN_81",
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{
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"Sample ID":"PMN_82",
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"Sample ID":"PMN_83",
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{
"Subject ID":"_84",
"Sample ID":"PMN_84",
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"Sample ID":"PMN_85",
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{
"Subject ID":"_86",
"Sample ID":"PMN_86",
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{
"Subject ID":"_87",
"Sample ID":"PMN_87",
"Factors":{"Experimental Factors":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"PMN_87.mzXML"}
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{
"Subject ID":"_88",
"Sample ID":"PMN_88",
"Factors":{"Experimental Factors":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"PMN_88.mzXML"}
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{
"Subject ID":"_89",
"Sample ID":"PMN_89",
"Factors":{"Experimental Factors":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"PMN_89.mzXML"}
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{
"Subject ID":"_90",
"Sample ID":"PMN_90",
"Factors":{"Experimental Factors":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"PMN_90.mzXML"}
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{
"Subject ID":"_91",
"Sample ID":"PMN_91",
"Factors":{"Experimental Factors":"Control"},
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{
"Subject ID":"_92",
"Sample ID":"PMN_92",
"Factors":{"Experimental Factors":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"PMN_92.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_01",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_01.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_02",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_02.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_03",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_03.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_04",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_04.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_05",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_05.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_06",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_06.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_07",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_07.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_08",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_08.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_09",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_09.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_10",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_10.mzXML"}
},
{
"Subject ID":"Pool",
"Sample ID":"QC_pool_11",
"Factors":{"Experimental Factors":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC_pool_11.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"COVID-19 patient samples were obtained through the University of Texas Southwestern Medical Center biorepository. Sample collection from COVID-19 patients or healthy controls was performed according to procedures approved by the Institutional Review Board of the University of Texas Southwestern Medical Center (STU-2020-0375 for SARS-CoV2 Biorepository and STU 012014-040 to J. Moreland) and the UT Southwestern Biorepository. Neutrophils were isolated using Ficoll-paque density gradient centrifugation, dextran sedimentation and erythrocyte hypotonic lysis following standard procedures as previously described (Hook et al., 2021). The number of neutrophils in each sample was counted using a microscope before freezing. Samples were stored at -800 C until metabolite extraction.","SAMPLE_TYPE":"Neutrophils"},
"TREATMENT":{"TREATMENT_SUMMARY":"No treatment were done"},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites from pellets containing 2 million neutrophils were extracted with 100 μl of chilled solvent of 40:40:20 methanol:acetonitrile:water (v:v:v) per million cells. The cell pellet was resuspended in the extraction solvent, vortexed for 30’’, and freeze-thawed 3 times. Then the samples were centrifuged at 21,000 g for 15 minutes at 4 °C and the supernatant transferred to LC-MS autosampler vials."},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Liquid chromatography was performed using a Millipore ZIC-pHILIC column (5 mm, 2.1×150 mm) with a binary solvent system of 10 mM ammonium acetate in water, pH 9.8 (solvent A) and acetonitrile (solvent B) with a constant flow rate of 0.25 mL/min. The column was equilibrated with 90% solvent B. The liquid chromatography gradient was: 0–15 minutes linear ramp from 90% B to 30% B; 15–18 minutes isocratic flow of 30% B; 18–19 minutes linear ramp from 30% B to 90% B; 19–27 column regeneration with isocratic flow of 90% B.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Scientific QExactive HF-X hybrid quadrupole orbitrap high-resolution mass spectrometer (HRMS)","COLUMN_NAME":"Millipore ZIC-pHILIC column (5 mm, 2.1×150 mm)","SOLVENT_A":"100% water; 10 mM ammonium acetate, pH 9.8","SOLVENT_B":"100% acetonitrile","FLOW_GRADIENT":"0–15 minutes linear ramp from 90% B to 30% B; 15–18 minutes isocratic flow of 30% B; 18–19 minutes linear ramp from 30% B to 90% B; 19–27 column regeneration with isocratic flow of 90% B.","FLOW_RATE":"0.25 mL/min","COLUMN_TEMPERATURE":"40"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF-X Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"Polarity switching was used to detect both positive and negative ions. A pooled quality control (QC) sample was used through the LC-MS run interspersed with the neutrophil samples to monitor the quality and consistency of detection. All samples were randomized to avoid artifactual changes caused by systematic drift. For data acquired with the QExactive, chromatogram peak areas were integrated using Tracefinder (Thermo Scientific) for targeted analysis using an in-house database."},
"MS_METABOLITE_DATA":{
"Units":"MS reading",
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}
}