{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001032","ANALYSIS_ID":"AN001692","VERSION":"1","CREATED_ON":"August 9, 2018, 3:10 pm"},

"PROJECT":{"PROJECT_TITLE":"Single-cell Profiling of Cationic and Anionic Metabolites in Live Frog (Xenopus) Embryos using Microprobe Capillary Electrophoresis Mass Spectrometry","PROJECT_TYPE":"Metabolic profiling of anionic and cationic metabolites in single cells","PROJECT_SUMMARY":"The goal of this study was to enable the analysis of anionic and cationic metabolites from the same identified single cell in Xenopus laevis embryos. A 10 nL portion of identified animal-ventral (V1) cells was aspirated from 8-cell embryos, and metabolites were extracted from the aspirate, before characterization of cationic and anionic compounds using a custom-built capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry platform. A total of ~250 cationic molecular features and ~150 anionic molecular features were detected, including 76 metabolites that were identified in this study. Pathway analysis of the identified metabolites highlighted arginine-proline metabolism of significance.","INSTITUTE":"University of Maryland","DEPARTMENT":"Department of Chemistry & Biochemistry","LABORATORY":"Nemes Laboratory","LAST_NAME":"Nemes","FIRST_NAME":"Peter","ADDRESS":"0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742","EMAIL":"nemes@umd.edu","PHONE":"301-405-0373","FUNDING_SOURCE":"National Cancer Institute grant 7R03CA211635"},

"STUDY":{"STUDY_TITLE":"Single-cell Profiling of Cationic and Anionic Metabolites in Live Frog (Xenopus) Embryos using Microprobe Capillary Electrophoresis Mass Spectrometry","STUDY_TYPE":"Metabolic profiling of single cells","STUDY_SUMMARY":"The goal of this study was to enable the analysis of anionic and cationic metabolites from the same identified single cell in Xenopus laevis embryos. A 10 nL portion of identified animal-ventral (V1) cells was aspirated from 8-cell embryos, and metabolites were extracted from the aspirate, before characterization of cationic and anionic compounds using a custom-built capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry platform. A total of ~250 cationic molecular features and ~150 anionic molecular features were detected, including 76 metabolites that were identified in this study. Pathway analysis of the identified metabolites highlighted arginine-proline metabolism of significance.","INSTITUTE":"University of Maryland","DEPARTMENT":"Department of Chemistry & Biochemistry","LABORATORY":"Nemes Laboratory","LAST_NAME":"Nemes","FIRST_NAME":"Peter","ADDRESS":"0107 Chemistry Building 8051 Regents Drive","EMAIL":"nemes@umd.edu","PHONE":"3014050373","NUM_GROUPS":"4 biological replicates (each different cell from a different embryo) + 1-to-2 technical replicates (same extract analyzed multiple times)","TOTAL_SUBJECTS":"4 different V1 cells were analyzed, each from a different embryo"},

"SUBJECT":{"SUBJECT_TYPE":"Other","SUBJECT_SPECIES":"Xenopus laevis","TAXONOMY_ID":"8355","AGE_OR_AGE_RANGE":"Embryos were obtained from natural mating of frogs (Nasco)","WEIGHT_OR_WEIGHT_RANGE":"Sexually mature male and female frogs","GENDER":"Not applicable"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"2016-12-20_EP02 negative mode 8-cell embryo1",
"Sample ID":"V1E1T1N",
"Factors":{"Embryo Type":"WT"},
"Additional sample data":{"Biological Replicate Number":"1"}
},
{
"Subject ID":"2017-07-31_EP02 negative mode 8-cell embryo2.d",
"Sample ID":"V1E2T1N",
"Factors":{"Embryo Type":"WT"},
"Additional sample data":{"Biological Replicate Number":"2"}
},
{
"Subject ID":"2017-08-01_EP02 positive mode 8-cell embryo2.d",
"Sample ID":"V1E2T1P",
"Factors":{"Embryo Type":"WT"},
"Additional sample data":{"Biological Replicate Number":"2"}
},
{
"Subject ID":"2017-11-17_EP04 positive mode V1-E3.d",
"Sample ID":"V1E3T1P",
"Factors":{"Embryo Type":"WT"},
"Additional sample data":{"Biological Replicate Number":"3"}
},
{
"Subject ID":"2017-11-27_EP02 negative mode V1-E4.d",
"Sample ID":"V1E4T1N",
"Factors":{"Embryo Type":"WT"},
"Additional sample data":{"Biological Replicate Number":"4"}
},
{
"Subject ID":"2017-11-17_EP03 positive mode V1-E3-TR2.d",
"Sample ID":"V1E3T2P",
"Factors":{"Embryo Type":"WT"},
"Additional sample data":{"Biological Replicate Number":"3"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were identified based on morphology, pigmentation, and location in the embryo in comparison to established cell-fate maps for Xenopus laevis embryos. A portion of the identified V1 cell was microaspirated using a fabricated microcapillary.","COLLECTION_PROTOCOL_ID":"Portero 2018 Metabolomics Workbench Protocols FINAL 2018-08-08","COLLECTION_PROTOCOL_FILENAME":"nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf","SAMPLE_TYPE":"embryonic cell","COLLECTION_METHOD":"Microaspiration of cell content","COLLECTION_FREQUENCY":"1 collection per cell","COLLECTION_DURATION":"5 s for aspiration","VOLUMEORAMOUNT_COLLECTED":"Ca. 10 nL per aspiration","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"All protocols related to the handling and manipulation of animals were approved by the University of Maryland, College Park (College Park, MD). Embryos were dejellied using 2% cystine solution, cultured in 100% Steinberg's solution (media), and used without further treatment.","TREATMENT_PROTOCOL_ID":"IACUC # R-DEC-17-57","TREATMENT_PROTOCOL_FILENAME":"nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Ca. 10 nL of cell content were aspirated from identified cells. The aspirated material was ejected into ~4 uL of aqueous mixture of 40% acetonitrile and 40% methanol to extract metabolites.","SAMPLEPREP_PROTOCOL_FILENAME":"nemes_20180725_143242_PR_SP_Liu_2018_Metabolomics_Workbench_Protocol.pdf","PROCESSING_METHOD":"On ice, then extracts stored at -80 degC until analysis.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"In cold aqueous mixture of 40% acetonitrile and 40% methanol.","EXTRACT_ENRICHMENT":"none","EXTRACT_CLEANUP":"none","EXTRACT_STORAGE":"-80℃","SUBCELLULAR_LOCATION":"Unknown"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Metabolites were separated in a custom-built capillary electrophoresis (CE) system.","CHROMATOGRAPHY_TYPE":"CE","INSTRUMENT_NAME":"Custom-built CE system","COLUMN_NAME":"Bare fused silica capillary","COLUMN_TEMPERATURE":"Room temperature","SOLVENT_A":"During cationic separation, the background electrolyte used in postive ionization mode was 1% formic acid in water (isocratic).","INJECTION_TEMPERATURE":"Room temperature","SAMPLE_INJECTION":"Ca. 10 nL","ANALYTICAL_TIME":"45 min of separation","CAPILLARY_VOLTAGE":"During cationic separation, +19,000-20,000 V was applied on the inlet end of the CE capillary.","PRECONDITIONING":"Sodium hydroxide solution","SHEATH_LIQUID":"During cationic analysis, the electrospray sheath solution was 50% methanol with 0.1% formic acid."},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Nemes Laboratory","OPERATOR_NAME":"Erika Portero","SOFTWARE_VERSION":"Compass 4.3"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Bruker Impact HD","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_TEMPERATURE":"100 degC","CAPILLARY_VOLTAGE":"+1700 V during cationic analysis","MASS_ACCURACY":"<5 ppm","DATAFORMAT":"mzML","SCANNING_CYCLE":"2 Hz","SCANNING_RANGE":"mz 50-550"},

"MS_METABOLITE_DATA":{
"Units":"peak area",

"Data":[{"Metabolite":"Lysine","V1E2T1P":"18719536","V1E3T1P":"","V1E3T2P":"7011901"},{"Metabolite":"Arginine","V1E2T1P":"","V1E3T1P":"16969458","V1E3T2P":"34194288"},{"Metabolite":"Guanine","V1E2T1P":"","V1E3T1P":"19523818","V1E3T2P":"179979696"},{"Metabolite":"Pyridoxal","V1E2T1P":"2847430","V1E3T1P":"678385","V1E3T2P":"1816902"},{"Metabolite":"Creatine","V1E2T1P":"","V1E3T1P":"","V1E3T2P":"1315571"},{"Metabolite":"Alanine","V1E2T1P":"","V1E3T1P":"","V1E3T2P":""},{"Metabolite":"Asparagine","V1E2T1P":"","V1E3T1P":"","V1E3T2P":""},{"Metabolite":"Glutamine","V1E2T1P":"","V1E3T1P":"25867","V1E3T2P":"55428524"},{"Metabolite":"Glutamate","V1E2T1P":"","V1E3T1P":"278801","V1E3T2P":"256206176"},{"Metabolite":"Aspartic acid","V1E2T1P":"31290716","V1E3T1P":"","V1E3T2P":"66008124"},{"Metabolite":"Hypoxanthine","V1E2T1P":"154605728","V1E3T1P":"","V1E3T2P":"1385160"},{"Metabolite":"Hydroxyproline","V1E2T1P":"11474813","V1E3T1P":"","V1E3T2P":"98667"}],

"Metabolites":[{"Metabolite":"Lysine","Retention Index":"16.4","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"5962"},{"Metabolite":"Arginine","Retention Index":"17.08","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"6322"},{"Metabolite":"Guanine","Retention Index":"32.1","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"764"},{"Metabolite":"Pyridoxal","Retention Index":"34.1","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"1050"},{"Metabolite":"Creatine","Retention Index":"20.94","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"586"},{"Metabolite":"Alanine","Retention Index":"32.1","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"5950"},{"Metabolite":"Asparagine","Retention Index":"26.75","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"6267"},{"Metabolite":"Glutamine","Retention Index":"27.03","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"5961"},{"Metabolite":"Glutamate","Retention Index":"27.09","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"33032"},{"Metabolite":"Aspartic acid","Retention Index":"29.99","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"5960"},{"Metabolite":"Hypoxanthine","Retention Index":"65.4","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"7090"},{"Metabolite":"Hydroxyproline","Retention Index":"32.57","Moverz Quant":"","Local ID (CAS)":"","PubChem CID":"5810"}]
}

}