{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002724","ANALYSIS_ID":"AN004415","VERSION":"1","CREATED_ON":"June 6, 2023, 9:51 am"},

"PROJECT":{"PROJECT_TITLE":"Ceramides profile in HeLa overexpressing nSMase2 (SMPD3)","PROJECT_TYPE":"Lipidomics","PROJECT_SUMMARY":"This study aim to determine which species of ceramides are modified by overexpression of the protein neutral sphingomyelinase 2 (nSMase2, gene SMPD3). HeLa cells were transfected with a plasmid containing V5-tagged nSMase2. Lipids were extracted after 24h after transfection and the sphingolipid profile was determined by LC-MS/MS.","INSTITUTE":"Stony Brook University","DEPARTMENT":"Medicine","LABORATORY":"Daniel Canals","LAST_NAME":"Canals","FIRST_NAME":"Daniel","ADDRESS":"100 Nicolls Road, Stony Brook, NY, 11794, USA","EMAIL":"daniel.canals@stonybrookmedicine.edu","PHONE":"6312162903"},

"STUDY":{"STUDY_TITLE":"Ceramides profile in HeLa overexpressing nSMase2 (SMPD3)","STUDY_TYPE":"Lipidomics LC-MS/MS","STUDY_SUMMARY":"This study aim to determine which species of ceramides are modified by overexpression of the protein neutral sphingomyelinase 2 (nSMase2, gene SMPD3). HeLa cells were transfected with a plasmid containing V5-tagged nSMase2. Lipids were extracted after 24h after transfection and the sphingolipid profile was determined by LC-MS/MS.","INSTITUTE":"State University of New York","DEPARTMENT":"MEdicine","LABORATORY":"Daniel Canals","LAST_NAME":"Daniel","FIRST_NAME":"Canals","ADDRESS":"100 Nicolls Road","EMAIL":"daniel.canals@stonybrook.edu","PHONE":"6312162903"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"AO_01",
"Factors":{"Expression vector":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"AO_01.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"AO_02",
"Factors":{"Expression vector":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"AO_02.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"AO_03",
"Factors":{"Expression vector":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"AO_03.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"AO_13",
"Factors":{"Expression vector":"nSMase2-V5"},
"Additional sample data":{"RAW_FILE_NAME":"AO_13.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"AO_14",
"Factors":{"Expression vector":"nSMase2-V5"},
"Additional sample data":{"RAW_FILE_NAME":"AO_14.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"AO_15",
"Factors":{"Expression vector":"nSMase2-V5"},
"Additional sample data":{"RAW_FILE_NAME":"AO_15.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"ATCC HeLa - CCL-2","SAMPLE_TYPE":"Cultured cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Transfection with SPMD3 gene"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Ceramides were extracted using 2:3 70% Isopropanol: EthylAcetate. See protocol.docx for details.","PROCESSING_STORAGE_CONDITIONS":"-20℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Spectra C8SR (150 × 3.0 mm, 3um) (#S-3C8SR-FJ)","SOLVENT_A":"100% water; 0.2% formic acid ; 1mM ammonium formate","SOLVENT_B":"100% methanol; 0.2% formic acid ; 1mM ammonium formate","FLOW_GRADIENT":"0.5ml/min. 70%B. 5 min 90%B, 17 min 99%B, 26min 99%B, 26.5min 70% B. Stop at 35min.","FLOW_RATE":"0.5ml/min","COLUMN_TEMPERATURE":"37"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Quantiva","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Acquisition and Processing were done using TraceFinder Software."},

"MS_METABOLITE_DATA":{
"Units":"pmols",

"Data":[{"Metabolite":"C12-Cer","AO_01":"0.24","AO_02":"0.21","AO_03":"0.33","AO_13":"0.81","AO_14":"0.75","AO_15":"0.61"},{"Metabolite":"C14-Cer_x","AO_01":"5.8","AO_02":"5.06","AO_03":"4.65","AO_13":"21.98","AO_14":"20.07","AO_15":"13.74"},{"Metabolite":"C16-Cer_x","AO_01":"40.6","AO_02":"35.07","AO_03":"32.19","AO_13":"143.59","AO_14":"130.61","AO_15":"91.34"},{"Metabolite":"C18:1-Cer_x","AO_01":"1.95","AO_02":"1.44","AO_03":"1.42","AO_13":"5.46","AO_14":"5.19","AO_15":"3.88"},{"Metabolite":"C18-Cer_x","AO_01":"7.25","AO_02":"6.47","AO_03":"6.27","AO_13":"15.34","AO_14":"13.9","AO_15":"10.95"},{"Metabolite":"C20:1-Cer","AO_01":"0.95","AO_02":"0.75","AO_03":"0.75","AO_13":"3.28","AO_14":"3.03","AO_15":"2.28"},{"Metabolite":"C20-Cer_x","AO_01":"5.08","AO_02":"4.29","AO_03":"4.52","AO_13":"11.81","AO_14":"11.41","AO_15":"8.74"},{"Metabolite":"C22:1-Cer","AO_01":"4.82","AO_02":"4.4","AO_03":"4.3","AO_13":"25.93","AO_14":"23.32","AO_15":"17.44"},{"Metabolite":"C22-Cer_x","AO_01":"17.15","AO_02":"16.22","AO_03":"15.66","AO_13":"51.47","AO_14":"46.47","AO_15":"36.32"},{"Metabolite":"C24:1-Cer_x","AO_01":"81.88","AO_02":"75.68","AO_03":"75.94","AO_13":"290.75","AO_14":"266.38","AO_15":"214.13"},{"Metabolite":"C24-Cer_x","AO_01":"23.49","AO_02":"22.47","AO_03":"23.6","AO_13":"61.3","AO_14":"58.2","AO_15":"47.46"},{"Metabolite":"C26:1-Cer","AO_01":"4.08","AO_02":"4.07","AO_03":"4.07","AO_13":"8.72","AO_14":"8.45","AO_15":"7.8"},{"Metabolite":"C26-Cer","AO_01":"0.01","AO_02":"-0.05","AO_03":"-0.07","AO_13":"0.35","AO_14":"0.3","AO_15":"0.21"}],

"Metabolites":[{"Metabolite":"C12-Cer","RetentionTime":"12.21","m/z":"482.5","PubChemID":"5283562"},{"Metabolite":"C14-Cer_x","RetentionTime":"13.54","m/z":"510.5","PubChemID":"5282310"},{"Metabolite":"C16-Cer_x","RetentionTime":"14.93","m/z":"538.5","PubChemID":"2498"},{"Metabolite":"C18:1-Cer_x","RetentionTime":"15.3","m/z":"564.4","PubChemID":"5283563"},{"Metabolite":"C18-Cer_x","RetentionTime":"16.3","m/z":"566.5","PubChemID":"5283565"},{"Metabolite":"C20:1-Cer","RetentionTime":"16.6","m/z":"592.5","PubChemID":"249807232"},{"Metabolite":"C20-Cer_x","RetentionTime":"17.6","m/z":"594.5","PubChemID":"5283566  "},{"Metabolite":"C22:1-Cer","RetentionTime":"17.9","m/z":"620.6","PubChemID":"154573071  "},{"Metabolite":"C22-Cer_x","RetentionTime":"18.8","m/z":"622.6","PubChemID":"5283567  "},{"Metabolite":"C24:1-Cer_x","RetentionTime":"19.13","m/z":"648.7","PubChemID":"5283568 "},{"Metabolite":"C24-Cer_x","RetentionTime":"20.18","m/z":"650.7","PubChemID":"5283571"},{"Metabolite":"C26:1-Cer","RetentionTime":"20.3","m/z":"676.8","PubChemID":"154573078  "},{"Metabolite":"C26-Cer","RetentionTime":"20.36","m/z":"678.7","PubChemID":"5283570 "}]
}

}