{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000472","ANALYSIS_ID":"AN001823","VERSION":"1","CREATED_ON":"08-09-2023"},

"PROJECT":{"PROJECT_TITLE":"Degradation of Nucleotides under different chemical environments","PROJECT_SUMMARY":"The degradation kinetics of nucleotide triphosphates (ATP, GTP, UTP and CTP) were evaluated under boiling ethanol extraction conditions (95°C) during 0 to 300 minutes.","INSTITUTE":"University of Groningen","DEPARTMENT":"Analytical Biochemistry","LAST_NAME":"Bischoff","FIRST_NAME":"Rainer","ADDRESS":"Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands","EMAIL":"r.p.h.bischoff@rug.nl","PHONE":"NA","PUBLICATIONS":"Gil, A., Siegel, D., Bonsing-Vedelaar, S. et al. The degradation of nucleotide triphosphates extracted under boiling ethanol conditions is prevented by the yeast cellular matrix. Metabolomics (2017) 13:1. doi:10.1007/s11306-016-1140-4","DOI":"http://dx.doi.org/10.21228/M8CW21"},

"STUDY":{"STUDY_TITLE":"Effect of the culture medium on the degradation of nucleotide triphosphates","STUDY_TYPE":"Endpoint measurement","STUDY_SUMMARY":"The effect of the Verduyn culture medium on the degradation profiles of nucleotide triphosphates extracted under typical boiling ethanol conditions was evaluated.","INSTITUTE":"University of Groningen","DEPARTMENT":"Analytical Biochemistry","LAST_NAME":"Bischoff","FIRST_NAME":"Rainer","ADDRESS":"Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands","EMAIL":"r.p.h.bischoff@rug.nl","PHONE":"NA","SUBMIT_DATE":"2016-09-13"},

"SUBJECT":{"SUBJECT_TYPE":"Chemical","SUBJECT_SPECIES":"None","SUBJECT_COMMENTS":"Primary standards of nucleotide triphosphates (ATP, GTP, UTP and CTP)."},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"AG250615_23",
"Factors":{"Time (mins)":"15","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_24",
"Factors":{"Time (mins)":"15","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_25",
"Factors":{"Time (mins)":"15","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_26",
"Factors":{"Time (mins)":"15","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_66",
"Factors":{"Time (mins)":"15","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_68",
"Factors":{"Time (mins)":"15","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_70",
"Factors":{"Time (mins)":"15","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_72",
"Factors":{"Time (mins)":"15","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_37",
"Factors":{"Time (mins)":"15","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_38",
"Factors":{"Time (mins)":"15","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_39",
"Factors":{"Time (mins)":"15","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_40",
"Factors":{"Time (mins)":"15","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_15",
"Factors":{"Time (mins)":"15","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_17",
"Factors":{"Time (mins)":"15","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_19",
"Factors":{"Time (mins)":"15","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_21",
"Factors":{"Time (mins)":"15","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_18",
"Factors":{"Time (mins)":"-","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_19",
"Factors":{"Time (mins)":"-","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_20",
"Factors":{"Time (mins)":"-","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG250615_21",
"Factors":{"Time (mins)":"-","Nucleotide":"ATP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_58",
"Factors":{"Time (mins)":"-","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_60",
"Factors":{"Time (mins)":"-","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_62",
"Factors":{"Time (mins)":"-","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_64",
"Factors":{"Time (mins)":"-","Nucleotide":"CTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_32",
"Factors":{"Time (mins)":"-","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_33",
"Factors":{"Time (mins)":"-","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_34",
"Factors":{"Time (mins)":"-","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG150715_35",
"Factors":{"Time (mins)":"-","Nucleotide":"GTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_11",
"Factors":{"Time (mins)":"-","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_13",
"Factors":{"Time (mins)":"-","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_7",
"Factors":{"Time (mins)":"-","Nucleotide":"UTP"}
},
{
"Subject ID":"-",
"Sample ID":"AG200715_9",
"Factors":{"Time (mins)":"-","Nucleotide":"UTP"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"None"},

"TREATMENT":{"TREATMENT_SUMMARY":"Pure solutions of nucleotide triphosphates (ATP, GTP, CTP and UTP) were incubated under boiling ethanol conditions (95°C) during 0, 5, 10, 20, 30, 60, 120, 180, 240 and 300 minutes.","TREATMENT":"Abiotic"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Tubes containing 496 µL of 75% (aq) ethanol were preheated at 95°C for 5 min, followed by the addition of 4 µL of each nucleotide standard solution (500 µM) and vigorous mixing. 4 µL of solutions “A” to “H” were added to the reaction mixture and the samples were incubated at 95°C under shaking for 0 and 15 min. Reactions were stopped by snap-freezing in liquid nitrogen and samples were stored on dry ice. Subsequently, samples were thawed and 20 µL of the 13C15N-labeled internal standard solution were added for quantitative analysis. Excess solvent was evaporated under a stream of nitrogen without heating. Finally, samples were reconstituted in 200 µL of acetonitrile-water 70:30 and stored at –40°C until analysis by LC-MS. After the experimental procedure the final concentration of all components in solutions “A” to “H” was 10 µM. Compounds to be tested were divided into eight groups containing approximately ten compounds each, mainly comprising major central carbon metabolites including amino acids, organic acids, sugar phosphates, coenzymes, etc (Table 1).","PROCESSING_METHOD":"Preparation of reagents, dilution, solvent removal under a stream of nitrogen without heating and reconstitution","EXTRACTION_METHOD":"Boiling ethanol (95°C)","EXTRACT_ENRICHMENT":"Evaporation of excess of solvent under a stream of nitrogen without heating.","EXTRACT_STORAGE":"-40C","SAMPLE_RESUSPENSION":"200 µL of acetonitrile-water 70:30"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Untargeted HILIC Method","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Phenomenex Luna NH2 (100 x 2.0mm,3um)","COLUMN_TEMPERATURE":"20C","FLOW_GRADIENT":"30% eluent A to 99% eluent A in 8 min, followed by isocratic elution at 99% eluent A until 14 min. A conditioning cycle of 6 min with the initial proportions of eluents A and B was performed prior to the next analysis.","FLOW_RATE":"0.25 mL/min","SAMPLE_INJECTION":"10 µL","SOLVENT_A":"100% water; 5 mM ammonium acetate, pH 9.9","SOLVENT_B":"100% acetonitrile","ANALYTICAL_TIME":"20 min","CHROMATOGRAPHY_TYPE":"HILIC"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","SOFTWARE_VERSION":"MassLynx 4.1"},

"MS":{"INSTRUMENT_NAME":"Waters Synapt G2 Si QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","CAPILLARY_VOLTAGE":"2KV","COLLISION_ENERGY":"2 V for the low-collision energy scan, and 10–30 V for the high-collision energy scan","DRY_GAS_FLOW":"Argon","SOURCE_TEMPERATURE":"150C","DESOLVATION_TEMPERATURE":"400C","SCAN_RANGE_MOVERZ":"50 to 1200 Da"},

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

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