{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000246","ANALYSIS_ID":"AN000384","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Mammalian Suspension-Cultured Cellular Metabolomics Workflow","PROJECT_TYPE":"Metabolomics, Lipidomics, Untargeted","PROJECT_SUMMARY":"A workflow was optimized for the sample preparation of a single cell pellet for both metabolomics and lipidomics analysis. Jurkat T-lymphocyte were washed with various rinsing solutions and the lipids extracted using lipid extraction protocols to allow for the most reproducible and quantitative","INSTITUTE":"University of Florida","DEPARTMENT":"Dept. of Chemistry/SECIM","LABORATORY":"Biomedical Mass Spectrometry Lab","LAST_NAME":"Yost","FIRST_NAME":"Richard","ADDRESS":"P.O. Box 117200, Gainesville, FL 32611","EMAIL":"ryost@aa.ufl.edu","PHONE":"(352) 392-0515","FUNDING_SOURCE":"JDRF Research Grant"},

"STUDY":{"STUDY_TITLE":"Lipid Extraction Efficiency Comparison","STUDY_TYPE":"Lipid Extraction Efficiency Comparison","STUDY_SUMMARY":"Aliquots of Jurkat T-lymphocyte cells were extracted using the Folch or Matyash at different total volumes and run in triplicate to calculate the extraction for each method.","INSTITUTE":"University of Florida","DEPARTMENT":"Dept. of Chemistry/SECIM","LABORATORY":"Biomedical Mass Spectrometry Lab","LAST_NAME":"Ulmer","FIRST_NAME":"Candice","ADDRESS":"R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245","EMAIL":"czulmer@chem.ufl.edu","PHONE":"(352) 392-0515","NUM_GROUPS":"4","TOTAL_SUBJECTS":"12"},

"SUBJECT":{"SUBJECT_TYPE":"Human cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","CELL_BIOSOURCE_OR_SUPPLIER":"ATCC - Supplier","SUBJECT_COMMENTS":"P?+10","CELL_PRIMARY_IMMORTALIZED":"immortalized","CELL_PASSAGE_NUMBER":"P?+10","CELL_COUNTS":"P?+10","SPECIES_GROUP":"Human"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"folch_high",
"Factors":{"Extraction Method":"Folch"}
},
{
"Subject ID":"-",
"Sample ID":"folch_low",
"Factors":{"Extraction Method":"Folch"}
},
{
"Subject ID":"-",
"Sample ID":"mtbe_high",
"Factors":{"Extraction Method":"Matyash"}
},
{
"Subject ID":"-",
"Sample ID":"mtbe_low",
"Factors":{"Extraction Method":"Matyash"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Cells - Jurkat, Clone E6-1","COLLECTION_METHOD":"Centrifugation","COLLECTION_FREQUENCY":"1200 rpm","COLLECTION_DURATION":"5 min","VOLUMEORAMOUNT_COLLECTED":"10 mL of cell suspension","STORAGE_CONDITIONS":"-80°C","TISSUE_CELL_QUANTITY_TAKEN":"1e6 cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"-","CELL_STORAGE":"Liquid Nitrogen, 5% DMSO","CELL_GROWTH_CONTAINER":"10 cm2 culture dish","CELL_MEDIA":"RPMI 1640","CELL_ENVIR_COND":"95% humidity, 5% CO2","CELL_HARVESTING":"centrifugation"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cells were extracted using either the Folch or Matyash method. The total volume MeOH in each extraction method was varied (0.5 mL or 2.0 mL) while the ratio of to the other solvents was maintained.","SAMPLEPREP_PROTOCOL_FILENAME":"SOP_LipidExtractionProtocol.pdf","PROCESSING_METHOD":"cell lysis","PROCESSING_STORAGE_CONDITIONS":"on ice","EXTRACTION_METHOD":"Folch or Matyash lipid extraction method","SAMPLE_RESUSPENSION":"100 μL of IPA","SAMPLE_SPIKING":"internal standards: lysophosphatidylcholine (LPC 17:0 and LPC 19:0), (PC 17:0/17:0 and PC 19:0/19:0), phosphatidylethanolamine (PE 15:0/15:0 and PE phosphatidylserine (PS 14:0/14:0 and PS 17:0/17:0), and phosphatidylglycerol 14:0/14:0 and PG 17:0/17:0), triacylglyceride (TG 15:0/15:0/15:0 and TG","CELL_TYPE":"Jurkat, Clone E6-1"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Reversed Phase","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"Supelco Analytical Titan C18 column","METHODS_FILENAME":"m_lipid_pos_switch_100","COLUMN_PRESSURE":"1241 bar (max)","COLUMN_TEMPERATURE":"30 C","FLOW_GRADIENT":"32% B at 0 min, 40% B at 1 min, a hold at 40% B until 1.5 min, 45% B at 4 min, B at 5 min, 60% B at 8 min, 70% B at 11 min, and 80% B at 14 min","FLOW_RATE":"0.5 mL/min","INJECTION_TEMPERATURE":"4 C","SAMPLE_INJECTION":"2 μL","SOLVENT_A":"60:40 acetonitrile:water with 0.1% formic acid and    10 mM ammonium formate","SOLVENT_B":"90:8:2 isopropanol:acetonitrile:water with 0.1% formic acid and 10 mM ammonium","ANALYTICAL_TIME":"21 min","RANDOMIZATION_ORDER":"3,10,12,11,8,6,5,4,7,9,2,1"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Biomedical Mass Spectrometry Lab","ACQUISITION_DATE":"7/11-12/2014","ACQUISITION_PARAMETERS_FILE":"QE1_CZU_08_sequence","SOFTWARE_VERSION":"Xcalibur 2.2","OPERATOR_NAME":"Candice Ulmer","DETECTOR_TYPE":"orbitrap","DATA_FORMAT":".raw"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_TEMPERATURE":"320","DRY_GAS_FLOW":"30","MASS_ACCURACY":"<2 ppm","SPRAY_VOLTAGE":"3.5 kV","DESOLVATION_GAS_FLOW":".raw","SCAN_RANGE_MOVERZ":"100-1500","SKIMMER_VOLTAGE":"15 V"},

"MS_METABOLITE_DATA":{
"Units":"Peak Area",

"Data":[{"Metabolite":"PC(17:0/0:0)+H","folch_high":"2367239080.0000","folch_low":"1173754270.0000","mtbe_high":"1349160679.0000","mtbe_low":"787697999.8000"},{"Metabolite":"PC(17:0/17:0)+H","folch_high":"2347308996.0000","folch_low":"853638932.8000","mtbe_high":"619440512.5000","mtbe_low":"271569348.2000"},{"Metabolite":"PC(19:0/0:0)+H","folch_high":"2714419478.0000","folch_low":"1279452311.0000","mtbe_high":"826034899.3000","mtbe_low":"458158853.3000"},{"Metabolite":"PC(19:0/19:0)+H","folch_high":"3341173680.0000","folch_low":"1719493942.0000","mtbe_high":"1523319934.0000","mtbe_low":"639825587.2000"},{"Metabolite":"PE(15:0/15:0)+H","folch_high":"1251236443.0000","folch_low":"847868482.0000","mtbe_high":"614580873.4000","mtbe_low":"301764514.4000"},{"Metabolite":"PE(17:0/17:0)+H","folch_high":"248393150.0000","folch_low":"197939185.6000","mtbe_high":"188878695.4000","mtbe_low":"74619507.9800"},{"Metabolite":"PG(14:0/14:0)+NH4","folch_high":"531616976.5000","folch_low":"258579094.0000","mtbe_high":"171127089.2000","mtbe_low":"74833623.0300"},{"Metabolite":"PG(17:0/17:0)+NH4","folch_high":"342305741.2000","folch_low":"120563696.2000","mtbe_high":"110239109.1000","mtbe_low":"53441496.3700"},{"Metabolite":"PS(14:0/14:0)+H","folch_high":"153015056.3000","folch_low":"78399531.4900","mtbe_high":"28328397.3300","mtbe_low":"27476440.3400"},{"Metabolite":"PS(17:0/17:0)+H","folch_high":"88931263.7900","folch_low":"27861723.9800","mtbe_high":"12980051.4200","mtbe_low":"12649316.6200"},{"Metabolite":"TG(15:0/15:0/15:0)+NH4","folch_high":"2722439373.0000","folch_low":"2007178451.0000","mtbe_high":"653556766.3000","mtbe_low":"385216121.0000"},{"Metabolite":"TG(17:0/17:0/17:0)+NH4","folch_high":"2420850736.0000","folch_low":"1928633721.0000","mtbe_high":"829918104.5000","mtbe_low":"301486809.6000"}],

"Metabolites":[{"Metabolite":"PC(17:0/0:0)+H","moverz_quant":"510.3553","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PC(17:0/17:0)+H","moverz_quant":"762.6007","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PC(19:0/0:0)+H","moverz_quant":"538.3866","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PC(19:0/19:0)+H","moverz_quant":"818.6633","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PE(15:0/15:0)+H","moverz_quant":"720.5537","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PE(17:0/17:0)+H","moverz_quant":"664.4911","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PG(14:0/14:0)+NH4","moverz_quant":"768.5749","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PG(17:0/17:0)+NH4","moverz_quant":"684.481","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PS(14:0/14:0)+H","moverz_quant":"680.4496","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"PS(17:0/17:0)+H","moverz_quant":"764.5435","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"TG(15:0/15:0/15:0)+NH4","moverz_quant":"866.8171","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"TG(17:0/17:0/17:0)+NH4","moverz_quant":"782.7232","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"}]
}

}