{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000140","ANALYSIS_ID":"AN000222","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":"Cell Rinsing Solution Comparison","STUDY_TYPE":"Cell Rinsing Solution Comparison","STUDY_SUMMARY":"Aliquots of Jurkat T-lymphocyte cells were washed with 5 different rinsing (0.3% amm. formate, 0.3% amm. acetate, 0.9% NaCl, 1 M PBS, 100 mM PBS) and ran triplicate to monitor the effect of ion suppression on the electrospray signal.","INSTITUTE":"University of Florida","DEPARTMENT":"Dept. of Chemistry/SECIM","LABORATORY":"Biomedical Mass Spectrometry Lab","LAST_NAME":"Ulmer","FIRST_NAME":"Candice","ADDRESS":"P.O. Box 117200, Gainesville, FL 32611","EMAIL":"czulmer@chem.ufl.edu","PHONE":"(352) 392-0515","NUM_GROUPS":"5","TOTAL_SUBJECTS":"15"},

"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"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"amm_acetate",
"Factors":{"rinsing_solution":"0.3% ammonium acetate"},
"Additional sample data":{"subject_type":"Human","cell_line":"Jurkat T-lymphocyte"}
},
{
"Subject ID":"-",
"Sample ID":"amm_form",
"Factors":{"rinsing_solution":"0.3% ammonium formate"},
"Additional sample data":{"subject_type":"Human","cell_line":"Jurkat T-lymphocyte"}
},
{
"Subject ID":"-",
"Sample ID":"nacl",
"Factors":{"rinsing_solution":"0.9% NaCl"},
"Additional sample data":{"subject_type":"Human","cell_line":"Jurkat T-lymphocyte"}
},
{
"Subject ID":"-",
"Sample ID":"hepes",
"Factors":{"rinsing_solution":"100 mM HEPES"},
"Additional sample data":{"subject_type":"Human","cell_line":"Jurkat T-lymphocyte"}
},
{
"Subject ID":"-",
"Sample ID":"pbs",
"Factors":{"rinsing_solution":"1 M PBS"},
"Additional sample data":{"subject_type":"Human","cell_line":"Jurkat T-lymphocyte"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Jurkat cells, Clone E6-1","COLLECTION_METHOD":"Centrifugation","COLLECTION_FREQUENCY":"1200 rpm","COLLECTION_DURATION":"5 min.","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"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"80% MeOH metabolite extraction","SAMPLEPREP_PROTOCOL_ID":"SOP_PP_02","SAMPLEPREP_PROTOCOL_FILENAME":"SOP_PP_02_CZU.pdf","PROCESSING_METHOD":"cell lysis","PROCESSING_STORAGE_CONDITIONS":"on ice","EXTRACTION_METHOD":"80% MeOH","SAMPLE_RESUSPENSION":"30 ?L 0.1% formic acid in water","SAMPLE_SPIKING":"internal standards: (1) L-tryptophan-2,3,3-d3; (2) creatine-d3; (3) (4) caffeine-d3","CELL_TYPE":"Jurkat, Clone E6-1"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Reversed phase","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)","METHODS_FILENAME":"PFP-metabolomics-pos-350","COLUMN_PRESSURE":"800 bar (max)","COLUMN_TEMPERATURE":"30 C","FLOW_RATE":"0.35 mL/min","INJECTION_TEMPERATURE":"4 C","SAMPLE_INJECTION":"5 ?L","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"acetonitrile","ANALYTICAL_TIME":"18 min","RANDOMIZATION_ORDER":"3,5,7,2,12,10,15,9,13,14,4,8,6,1,11"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Biomedical Mass Spectrometry Lab","ACQUISITION_DATE":"12/7-8/2014","ACQUISITION_PARAMETERS_FILE":"QE1_CZU_17_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":"45","MASS_ACCURACY":"<2 ppm","SPRAY_VOLTAGE":"3.5 kV","DATAFORMAT":".raw","SCAN_RANGE_MOVERZ":"70-700","SKIMMER_VOLTAGE":"15 V"},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[{"Metabolite":"arginine","amm_acetate":"82331783.8000","amm_form":"31128891.8800","nacl":"97148010.2600","hepes":"22627002.0200","pbs":"20218282.3900"},{"Metabolite":"carnitine","amm_acetate":"14772456.7000","amm_form":"12691064.7000","nacl":"32000523.6600","hepes":"2585.1800","pbs":"9175332.2330"},{"Metabolite":"glutamine","amm_acetate":"1472163.7250","amm_form":"333339.8877","nacl":"333817.2587","hepes":"0.0000","pbs":"121125.9862"},{"Metabolite":"guanine","amm_acetate":"24811119.8600","amm_form":"12239277.2200","nacl":"13725598.6900","hepes":"0.0000","pbs":"9437603.1050"},{"Metabolite":"lysine","amm_acetate":"12310097.2100","amm_form":"4773283.9540","nacl":"2616477.5780","hepes":"7002565.3670","pbs":"1257819.2300"},{"Metabolite":"methionine","amm_acetate":"15530161.7700","amm_form":"24830289.6800","nacl":"2643381.9230","hepes":"13997592.8400","pbs":"179959.8205"},{"Metabolite":"nicotinamide","amm_acetate":"21216139.1200","amm_form":"7186481.7880","nacl":"19862303.7500","hepes":"20869738.8900","pbs":"6389141.3640"},{"Metabolite":"phenylalanine","amm_acetate":"50519131.1000","amm_form":"60219019.4800","nacl":"433334030.4000","hepes":"157476421.8000","pbs":"54695090.6300"},{"Metabolite":"proline","amm_acetate":"86469443.0700","amm_form":"54504149.6000","nacl":"151641969.9000","hepes":"3302296.6950","pbs":"43720506.3300"},{"Metabolite":"thiamin","amm_acetate":"6181644.5680","amm_form":"6809092.6300","nacl":"19012120.1000","hepes":"8987762.8830","pbs":"3621895.8810"},{"Metabolite":"tryptophan","amm_acetate":"10703570.3200","amm_form":"11281477.3600","nacl":"37715472.4200","hepes":"20951470.4500","pbs":"7576416.9890"},{"Metabolite":"tyrosine","amm_acetate":"32197745.4200","amm_form":"31245442.6800","nacl":"113835764.2000","hepes":"41472505.7600","pbs":"22825400.4600"}],

"Metabolites":[{"Metabolite":"arginine","moverz_quant":"175.119","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"carnitine","moverz_quant":"162.1125","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"glutamine","moverz_quant":"148.0604","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"guanine","moverz_quant":"174.0386","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"lysine","moverz_quant":"147.1128","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"methionine","moverz_quant":"150.0583","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"nicotinamide","moverz_quant":"123.0553","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"phenylalanine","moverz_quant":"166.0863","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"proline","moverz_quant":"116.0706","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"thiamin","moverz_quant":"265.1118","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"tryptophan","moverz_quant":"205.0972","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"},{"Metabolite":"tyrosine","moverz_quant":"204.0631","ri":"","ri_type":"","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"","other_id_type":"UFLORIDA_FEATURE"}]
}

}