{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001878","ANALYSIS_ID":"AN003082","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Babesia merozoite targeted metabolomics project","PROJECT_TYPE":"Characterization of the central carbon metabolism and associated pathways","PROJECT_SUMMARY":"The project aims to detect polar metabolites corresponding to metabolites present in isolated merozoites of the apicomplexan parasite Babesia divergens using liquid chromatography coupled to a triple-quad mass spectrometer and defined transitions for target metabolites of relevance","INSTITUTE":"CEU San Pablo University","DEPARTMENT":"Departamento de Quimica y Bioquimica","LABORATORY":"Centro de Metabolomica y Bioanalisis (CEMBIO)","LAST_NAME":"Fernandez","FIRST_NAME":"Miguel","ADDRESS":"Universidad CEU San Pablo, Campus de Montepríncipe, Alcorcón, Madrid, 28925, Spain","EMAIL":"mig.fernandez.ce@ceindo.ceu.es","PHONE":"913724711","DOI":"http://dx.doi.org/10.21228/M8NX2V"},

"STUDY":{"STUDY_TITLE":"Targeted analysis of Babesia divergens merozoites","STUDY_SUMMARY":"The study comprehends two consecutive LC-QqQ/MS analyses of Babesia divergens merozoite extracts isolated from B. divergens infected red blood cell cultures performed under identical chromatographic conditions and targeting distinct transitions corresponding to metabolites from specific pathways including the glycolysis, the TCA cycle, the pentose phosphate pathway, purine and pyrimidine biosynthesis and amino acid metabolism.","INSTITUTE":"Universidad CEU San Pablo","DEPARTMENT":"Departamento de Quimica y Bioquimica","LABORATORY":"Centro de Metabolomica y Bioanalisis (CEMBIO)","LAST_NAME":"Fernandez","FIRST_NAME":"Miguel","ADDRESS":"Universidad CEU San Pablo","EMAIL":"mig.fernandez.ce@ceindo.ceu.es","PHONE":"690090778","SUBMIT_DATE":"2020-12-16"},

"SUBJECT":{"SUBJECT_TYPE":"Other organism","SUBJECT_SPECIES":"Babesia divergens","TAXONOMY_ID":"32595","GENOTYPE_STRAIN":"Rouen 1986"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"mero_1",
"Sample ID":"bdivrou_mero_1_met_1",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_1_met_1.d"}
},
{
"Subject ID":"mero_1",
"Sample ID":"bdivrou_mero_1_met_2",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_1_met_2.d"}
},
{
"Subject ID":"mero_2",
"Sample ID":"bdivrou_mero_2_met_1",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_2_met_1.d"}
},
{
"Subject ID":"mero_2",
"Sample ID":"bdivrou_mero_2_met_2",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_2_met_2.d"}
},
{
"Subject ID":"mero_3",
"Sample ID":"bdivrou_mero_3_met_1",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_3_met_1.d"}
},
{
"Subject ID":"mero_3",
"Sample ID":"bdivrou_mero_3_met_2",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_3_met_2.d"}
},
{
"Subject ID":"mero_4",
"Sample ID":"bdivrou_mero_4_met_1",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_4_met_1.d"}
},
{
"Subject ID":"mero_4",
"Sample ID":"bdivrou_mero_4_met_2",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_4_met_2.d"}
},
{
"Subject ID":"mero_5",
"Sample ID":"bdivrou_mero_5_met_1",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_5_met_1.d"}
},
{
"Subject ID":"mero_5",
"Sample ID":"bdivrou_mero_5_met_2",
"Factors":{"Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME":"bdivrou_mero_5_met_2.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Merozoites were isolated from B. divergens infected erythrocite (iRBC) cultures at 40% parasitemia. The content from iRBC culture flasks was transferred to Falcon tubes and spinned at 600 x g and 4 ºC for 5 min. Then, supernatants were filtered once using 5 μm filters and twice using 1.2 μm filters (Versapor membranes) with the help of a 1 mL syringe. Subsequently, the resulting volume was spinned on a Falcon tube at 2000 x g and 4 ºC for 2 min. The supernatants were discarded, and merozoite-containing pellets were placed on ice.","SAMPLE_TYPE":"merozoites isolated from RBC"},

"TREATMENT":{"TREATMENT_SUMMARY":"Since this was a qualitative study aiming to characterize specific metabolites from the Babesia divergens merozoites, only one sample group was included and no treatment was performed"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolite extraction and quenching: four volumes of cold methanol were added to one volume isolated B. divergens merozoite pellets placed on ice and quickly mixed using a high speed vortex. Then, samples were placed in an ice bath for 10 min, Subsequently, samples were transferred to liquid nitrogen for 10 min and thawed in an ice bath for 10 min (this freeze-thaw cycle was repeated two times). Samples were then centrifuged at 5725 x g and 4 ºC for 5 min. Supernatants containing the metabolite extracts were transferred to new tubes, while the remaining pellets were re-extracted twice by adding 400 μL of cold methanol and undergoing the liquid nitrogen freeze-thaw cycles described above. Supernatants obtained for each biological replicate were combined and filtered through 0.22 μm nylon syringe filters and stored at -80 ºC until use. Prior to LC-QqQ/MS analysis, supernatants underwent LC-QqQ/MS-specific sample preparation. First supernatants were thawed on ice and vortex mixed for 2 min. On ice, 300 µL of each supernatant were transferred to LC/MS vials and evaporated using a vacuum concentrator at <10 bar for 2h. The dried extracts were then reconstituted in 60 µL of Milli-Q water with the help of an ultrasonic bath for 5 min. Then, samples were subjected to LC-QqQ/MS analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The chromatographic method consists on a subtle adaptation of the Agilent dMRM method, which uses tributylamine as an ion pairing reagent (for more information, see https://www.agilent.com/cs/library/technicaloverviews/public/5991-6482EN.pdf)","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)","CHROMATOGRAPHY_TYPE":"Reversed phase"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6460 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","MS_COMMENTS":"Method 1: Data was acquired in MRM mode. To achieve a higher signal from low-abundance metabolites, transitions corresponding to metabolites of interests were separated in two MS methods (see method 2). Transitions utilized in this study are subtle modifications of the transition dataset contained in the Agilent dMRM database and method (see https://www.agilent.com/cs/library/technicaloverviews/public/5991-6482EN.pdf). Feature assignment was performed by matching transitions and RT with these contained in the Agilent dMRM Database and Method, and further confirmed by addition of authentic MS-grade standards. The software workflow included user visualization in Agilent MassHunter Workstation Software Qualitative Analysis (version B.09.00), and further compound integration using Agilent MassHunter Workstation Software Quantitative Analysis (version B.09.00). Only metabolites with signal-to-noise ratio higher than 3 (limit of detection) were reported.","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"blank-substracted abundances",

"Data":[{"Metabolite":"2_3-Dihydroxyisovalerate","bdivrou_mero_1_met_2":"2410.0000","bdivrou_mero_2_met_2":"2838.0000","bdivrou_mero_3_met_2":"2070.0000","bdivrou_mero_4_met_2":"2793.0000","bdivrou_mero_5_met_2":"1902.0000"},{"Metabolite":"2-Deoxycytidine-5^-monophosphate","bdivrou_mero_1_met_2":"2149.0000","bdivrou_mero_2_met_2":"1911.0000","bdivrou_mero_3_met_2":"1462.0000","bdivrou_mero_4_met_2":"2053.0000","bdivrou_mero_5_met_2":"1337.0000"},{"Metabolite":"2-Deoxyuridine","bdivrou_mero_1_met_2":"1075.0000","bdivrou_mero_2_met_2":"1067.0000","bdivrou_mero_3_met_2":"1154.0000","bdivrou_mero_4_met_2":"1325.0000","bdivrou_mero_5_met_2":"1228.0000"},{"Metabolite":"4-Pyridoxic acid","bdivrou_mero_1_met_2":"1421.5000","bdivrou_mero_2_met_2":"1525.5000","bdivrou_mero_3_met_2":"1337.5000","bdivrou_mero_4_met_2":"945.5000","bdivrou_mero_5_met_2":"1115.5000"},{"Metabolite":"5^-Deoxy-5^-(methylthio)adenosine","bdivrou_mero_1_met_2":"2856.0000","bdivrou_mero_2_met_2":"1421.0000","bdivrou_mero_3_met_2":"1680.0000","bdivrou_mero_4_met_2":"2985.0000","bdivrou_mero_5_met_2":"1841.0000"},{"Metabolite":"Adenosine-3^_5^-cyclic monophosphate","bdivrou_mero_1_met_2":"561.0000","bdivrou_mero_2_met_2":"1569.0000","bdivrou_mero_3_met_2":"515.0000","bdivrou_mero_4_met_2":"1310.0000","bdivrou_mero_5_met_2":"957.0000"},{"Metabolite":"Carnitine","bdivrou_mero_1_met_2":"525.0000","bdivrou_mero_2_met_2":"304.0000","bdivrou_mero_3_met_2":"227.0000","bdivrou_mero_4_met_2":"328.0000","bdivrou_mero_5_met_2":"293.0000"},{"Metabolite":"Creatine","bdivrou_mero_1_met_2":"3374.0000","bdivrou_mero_2_met_2":"3176.0000","bdivrou_mero_3_met_2":"2428.0000","bdivrou_mero_4_met_2":"2808.0000","bdivrou_mero_5_met_2":"2207.0000"},{"Metabolite":"Creatinine","bdivrou_mero_1_met_2":"675.0000","bdivrou_mero_2_met_2":"614.0000","bdivrou_mero_3_met_2":"554.0000","bdivrou_mero_4_met_2":"820.0000","bdivrou_mero_5_met_2":"814.0000"},{"Metabolite":"Cytidine-5^-monophosphate","bdivrou_mero_1_met_2":"3803.0000","bdivrou_mero_2_met_2":"3612.0000","bdivrou_mero_3_met_2":"2400.0000","bdivrou_mero_4_met_2":"3589.0000","bdivrou_mero_5_met_2":"2090.0000"},{"Metabolite":"Dihydroorotic acid","bdivrou_mero_1_met_2":"1576.0000","bdivrou_mero_2_met_2":"1114.0000","bdivrou_mero_3_met_2":"634.0000","bdivrou_mero_4_met_2":"872.0000","bdivrou_mero_5_met_2":"1184.0000"},{"Metabolite":"Dihydrosphingosine","bdivrou_mero_1_met_2":"2261.5000","bdivrou_mero_2_met_2":"1410.5000","bdivrou_mero_3_met_2":"1206.5000","bdivrou_mero_4_met_2":"2093.5000","bdivrou_mero_5_met_2":"1144.5000"},{"Metabolite":"gamma-Glutamylcysteine","bdivrou_mero_1_met_2":"","bdivrou_mero_2_met_2":"1641.0000","bdivrou_mero_3_met_2":"1725.0000","bdivrou_mero_4_met_2":"","bdivrou_mero_5_met_2":"1840.0000"},{"Metabolite":"Gluconic acid // Galactonic acid","bdivrou_mero_1_met_2":"769.5000","bdivrou_mero_2_met_2":"596.5000","bdivrou_mero_3_met_2":"499.5000","bdivrou_mero_4_met_2":"556.5000","bdivrou_mero_5_met_2":"334.5000"},{"Metabolite":"Glucosamine // Galactosamine","bdivrou_mero_1_met_2":"528.0000","bdivrou_mero_2_met_2":"1127.0000","bdivrou_mero_3_met_2":"316.0000","bdivrou_mero_4_met_2":"1059.0000","bdivrou_mero_5_met_2":"723.0000"},{"Metabolite":"Glucose-1-phosphate // Mannose-1-phosphate","bdivrou_mero_1_met_2":"2764.0000","bdivrou_mero_2_met_2":"1887.0000","bdivrou_mero_3_met_2":"1876.0000","bdivrou_mero_4_met_2":"2119.0000","bdivrou_mero_5_met_2":"1984.0000"},{"Metabolite":"Gluthathione (oxidized_ GSSG)","bdivrou_mero_1_met_2":"20624.0000","bdivrou_mero_2_met_2":"11784.0000","bdivrou_mero_3_met_2":"7741.0000","bdivrou_mero_4_met_2":"12481.0000","bdivrou_mero_5_met_2":"5273.0000"},{"Metabolite":"Glyceric acid","bdivrou_mero_1_met_2":"4610.0000","bdivrou_mero_2_met_2":"3228.0000","bdivrou_mero_3_met_2":"2735.0000","bdivrou_mero_4_met_2":"2743.0000","bdivrou_mero_5_met_2":"1964.0000"},{"Metabolite":"Guanine","bdivrou_mero_1_met_2":"916.5000","bdivrou_mero_2_met_2":"657.5000","bdivrou_mero_3_met_2":"423.5000","bdivrou_mero_4_met_2":"618.5000","bdivrou_mero_5_met_2":"566.5000"},{"Metabolite":"Guanosine","bdivrou_mero_1_met_2":"2108.0000","bdivrou_mero_2_met_2":"1747.0000","bdivrou_mero_3_met_2":"1216.0000","bdivrou_mero_4_met_2":"1482.0000","bdivrou_mero_5_met_2":"1288.0000"},{"Metabolite":"Hydroxyhippuric acid","bdivrou_mero_1_met_2":"2138.5000","bdivrou_mero_2_met_2":"1282.5000","bdivrou_mero_3_met_2":"802.5000","bdivrou_mero_4_met_2":"1269.5000","bdivrou_mero_5_met_2":"964.5000"},{"Metabolite":"Hypoxanthine","bdivrou_mero_1_met_2":"235797.0000","bdivrou_mero_2_met_2":"201272.0000","bdivrou_mero_3_met_2":"129019.0000","bdivrou_mero_4_met_2":"216173.0000","bdivrou_mero_5_met_2":"134377.0000"},{"Metabolite":"Indoline carboxylate","bdivrou_mero_1_met_2":"338.5000","bdivrou_mero_2_met_2":"848.5000","bdivrou_mero_3_met_2":"301.5000","bdivrou_mero_4_met_2":"110.5000","bdivrou_mero_5_met_2":"214.5000"},{"Metabolite":"Inosine","bdivrou_mero_1_met_2":"33004.0000","bdivrou_mero_2_met_2":"26946.0000","bdivrou_mero_3_met_2":"19733.0000","bdivrou_mero_4_met_2":"29731.0000","bdivrou_mero_5_met_2":"21178.0000"},{"Metabolite":"Inosine-5^-monophosphate","bdivrou_mero_1_met_2":"99144.0000","bdivrou_mero_2_met_2":"85968.0000","bdivrou_mero_3_met_2":"57616.0000","bdivrou_mero_4_met_2":"86931.0000","bdivrou_mero_5_met_2":"48697.0000"},{"Metabolite":"Inositol","bdivrou_mero_1_met_2":"1104653.5000","bdivrou_mero_2_met_2":"889014.5000","bdivrou_mero_3_met_2":"915508.5000","bdivrou_mero_4_met_2":"1100748.5000","bdivrou_mero_5_met_2":"949953.5000"},{"Metabolite":"Ketoisovaleric acid // Ketovaleric acid","bdivrou_mero_1_met_2":"55689.0000","bdivrou_mero_2_met_2":"48751.0000","bdivrou_mero_3_met_2":"35421.0000","bdivrou_mero_4_met_2":"55224.0000","bdivrou_mero_5_met_2":"31039.0000"},{"Metabolite":"Malonic acid","bdivrou_mero_1_met_2":"78502.0000","bdivrou_mero_2_met_2":"69729.0000","bdivrou_mero_3_met_2":"51996.0000","bdivrou_mero_4_met_2":"86915.0000","bdivrou_mero_5_met_2":"75221.0000"},{"Metabolite":"Mannose // Sorbose","bdivrou_mero_1_met_2":"9043.0000","bdivrou_mero_2_met_2":"8276.0000","bdivrou_mero_3_met_2":"7709.0000","bdivrou_mero_4_met_2":"9184.0000","bdivrou_mero_5_met_2":"9145.0000"},{"Metabolite":"N-Acetyl-glucosamine-6-phosphate // N-Acetyl-glucosamine-1-phosphate","bdivrou_mero_1_met_2":"1902.0000","bdivrou_mero_2_met_2":"2483.0000","bdivrou_mero_3_met_2":"1435.0000","bdivrou_mero_4_met_2":"2388.0000","bdivrou_mero_5_met_2":"990.0000"},{"Metabolite":"N-Acetylglucosamine // N-Acetylgalactosamine","bdivrou_mero_1_met_2":"93.0000","bdivrou_mero_2_met_2":"59.0000","bdivrou_mero_3_met_2":"120.0000","bdivrou_mero_4_met_2":"121.0000","bdivrou_mero_5_met_2":"176.0000"},{"Metabolite":"N-Acetylneuraminic acid","bdivrou_mero_1_met_2":"182.0000","bdivrou_mero_2_met_2":"298.0000","bdivrou_mero_3_met_2":"215.0000","bdivrou_mero_4_met_2":"320.0000","bdivrou_mero_5_met_2":"242.0000"},{"Metabolite":"N-Carbamoyl-DL-aspartic acid","bdivrou_mero_1_met_2":"11637.0000","bdivrou_mero_2_met_2":"8647.0000","bdivrou_mero_3_met_2":"7178.0000","bdivrou_mero_4_met_2":"10963.0000","bdivrou_mero_5_met_2":"6987.0000"},{"Metabolite":"Nicotinic acid","bdivrou_mero_1_met_2":"4114.0000","bdivrou_mero_2_met_2":"7941.0000","bdivrou_mero_3_met_2":"3457.0000","bdivrou_mero_4_met_2":"5027.0000","bdivrou_mero_5_met_2":"3938.0000"},{"Metabolite":"Nicotinic acid mononucleotide","bdivrou_mero_1_met_2":"3324.0000","bdivrou_mero_2_met_2":"1900.0000","bdivrou_mero_3_met_2":"1455.0000","bdivrou_mero_4_met_2":"2234.0000","bdivrou_mero_5_met_2":"1346.0000"},{"Metabolite":"o-glycosyl-glucose (Maltose // Cellobiose)","bdivrou_mero_1_met_2":"462.5000","bdivrou_mero_2_met_2":"634.5000","bdivrou_mero_3_met_2":"332.5000","bdivrou_mero_4_met_2":"306.5000","bdivrou_mero_5_met_2":"203.5000"},{"Metabolite":"Orotic acid","bdivrou_mero_1_met_2":"3834.5000","bdivrou_mero_2_met_2":"3960.5000","bdivrou_mero_3_met_2":"2803.5000","bdivrou_mero_4_met_2":"2766.5000","bdivrou_mero_5_met_2":"2765.5000"},{"Metabolite":"Pantothenic acid","bdivrou_mero_1_met_2":"5013.0000","bdivrou_mero_2_met_2":"4819.0000","bdivrou_mero_3_met_2":"3216.0000","bdivrou_mero_4_met_2":"5197.0000","bdivrou_mero_5_met_2":"3421.0000"},{"Metabolite":"Pentane-1_2_3_4_5-pentol (Arabitol // Xylitol // Ribitol)","bdivrou_mero_1_met_2":"139.0000","bdivrou_mero_2_met_2":"598.0000","bdivrou_mero_3_met_2":"96.0000","bdivrou_mero_4_met_2":"230.0000","bdivrou_mero_5_met_2":"198.0000"},{"Metabolite":"Phenylpyruvic acid","bdivrou_mero_1_met_2":"986.0000","bdivrou_mero_2_met_2":"949.0000","bdivrou_mero_3_met_2":"443.0000","bdivrou_mero_4_met_2":"451.0000","bdivrou_mero_5_met_2":"428.0000"},{"Metabolite":"p-hydroxybenzoic acid","bdivrou_mero_1_met_2":"169192.0000","bdivrou_mero_2_met_2":"181447.0000","bdivrou_mero_3_met_2":"125797.0000","bdivrou_mero_4_met_2":"184169.0000","bdivrou_mero_5_met_2":"122270.0000"},{"Metabolite":"Pyridoxal","bdivrou_mero_1_met_2":"5856.0000","bdivrou_mero_2_met_2":"6218.0000","bdivrou_mero_3_met_2":"3316.0000","bdivrou_mero_4_met_2":"5272.0000","bdivrou_mero_5_met_2":"3243.0000"},{"Metabolite":"Pyridoxal-5-phosphate","bdivrou_mero_1_met_2":"4334.0000","bdivrou_mero_2_met_2":"1985.0000","bdivrou_mero_3_met_2":"1672.0000","bdivrou_mero_4_met_2":"2814.0000","bdivrou_mero_5_met_2":"1065.0000"},{"Metabolite":"S-(5^-Adenosyl)homocysteine","bdivrou_mero_1_met_2":"745.0000","bdivrou_mero_2_met_2":"579.0000","bdivrou_mero_3_met_2":"358.0000","bdivrou_mero_4_met_2":"561.0000","bdivrou_mero_5_met_2":"399.0000"},{"Metabolite":"Taurine","bdivrou_mero_1_met_2":"1426.0000","bdivrou_mero_2_met_2":"1857.0000","bdivrou_mero_3_met_2":"1122.0000","bdivrou_mero_4_met_2":"1665.0000","bdivrou_mero_5_met_2":"1591.0000"},{"Metabolite":"Taurocholic acid","bdivrou_mero_1_met_2":"53.5000","bdivrou_mero_2_met_2":"56.5000","bdivrou_mero_3_met_2":"35.5000","bdivrou_mero_4_met_2":"59.5000","bdivrou_mero_5_met_2":"42.5000"},{"Metabolite":"Thiamine","bdivrou_mero_1_met_2":"1412.0000","bdivrou_mero_2_met_2":"778.0000","bdivrou_mero_3_met_2":"1120.0000","bdivrou_mero_4_met_2":"1745.0000","bdivrou_mero_5_met_2":"1426.0000"},{"Metabolite":"Thymidine","bdivrou_mero_1_met_2":"1584.0000","bdivrou_mero_2_met_2":"1687.0000","bdivrou_mero_3_met_2":"931.0000","bdivrou_mero_4_met_2":"1629.0000","bdivrou_mero_5_met_2":"1047.0000"},{"Metabolite":"Uridine","bdivrou_mero_1_met_2":"19358.0000","bdivrou_mero_2_met_2":"16206.0000","bdivrou_mero_3_met_2":"10107.0000","bdivrou_mero_4_met_2":"17895.0000","bdivrou_mero_5_met_2":"9972.0000"},{"Metabolite":"Uridine-5^-diphosphoglucose // Uridine 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}

}