{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001232","ANALYSIS_ID":"AN002050","VERSION":"1","CREATED_ON":"03-03-2022"},

"PROJECT":{"PROJECT_TITLE":"Combining stage - specificity and metabolomic profiling to advance drug discovery for malaria","PROJECT_TYPE":"LC-MS Metabolomics","PROJECT_SUMMARY":"Hydrophilic LC-MS analysis of compounds as part of functional examination of metabolic impact in relation to stage-specificity of antimalarials","INSTITUTE":"Pennsylvania State University","DEPARTMENT":"BMB","LABORATORY":"Llinás Laboratory","LAST_NAME":"Llinás","FIRST_NAME":"Manuel","ADDRESS":"W-122 Millennium Science Complex, Pollock Road","EMAIL":"eso5005@psu.edu","PHONE":"8148673527","FUNDING_SOURCE":"This work was supported by the Bill and Melinda Gates Foundation ( OPP1054480 ) , the Medicines for Malaria Venture ( 08/0015 ) and the National Institutes of Health (R37 AI50234, R01 AI109023, R01 AI124678; R33 AI127581)","DOI":"http://dx.doi.org/10.21228/M81X1W"},

"STUDY":{"STUDY_TITLE":"Combining stage - specificity and metabolomic profiling to advance drug discovery for malaria","STUDY_TYPE":"Drug Exposure","STUDY_SUMMARY":"Metabolic examination/confirmation of MoA stage-specificity observed in study","INSTITUTE":"Pennsylvania State University","DEPARTMENT":"BMB","LABORATORY":"Llinás Laboratory","LAST_NAME":"Owen","FIRST_NAME":"Edward","ADDRESS":"6014 Goldenrod Court","EMAIL":"eso5005@psu.edu","PHONE":"8144045235","SUBMIT_DATE":"2019-07-09"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Plasmodium falciparum","TAXONOMY_ID":"5833","GENOTYPE_STRAIN":"3D7","CELL_STRAIN_DETAILS":"MR4-3D7","SUBJECT_COMMENTS":"All were MACS seperated Trophozoite infected red blood cells","CELL_COUNTS":"1x10^8 per technical replicate"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-04072018",
"Factors":{"Drug treatment":"ATQ-04072018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-05102017",
"Factors":{"Drug treatment":"ATQ-05102017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-06022018",
"Factors":{"Drug treatment":"ATQ-06022018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-11022019",
"Factors":{"Drug treatment":"ATQ-11022019"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-11102018",
"Factors":{"Drug treatment":"ATQ-11102018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-16032017",
"Factors":{"Drug treatment":"ATQ-16032017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-18012018",
"Factors":{"Drug treatment":"ATQ-18012018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-18102017",
"Factors":{"Drug treatment":"ATQ-18102017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-21062017",
"Factors":{"Drug treatment":"ATQ-21062017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-22092017",
"Factors":{"Drug treatment":"ATQ-22092017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-26072017",
"Factors":{"Drug treatment":"ATQ-26072017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ATQ-27062018",
"Factors":{"Drug treatment":"ATQ-27062018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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"Factors":{"Drug treatment":"ATQ-29062017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"DHA-30012018",
"Factors":{"Drug treatment":"DHA-30012018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"Ferroquine-06022018",
"Factors":{"Drug treatment":"Ferroquine-06022018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"GNF-Pf-5660-27062018",
"Factors":{"Drug treatment":"GNF-Pf-5660-27062018"},
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"KAI407-29062017",
"Factors":{"Drug treatment":"KAI407-29062017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"Lumefantrine-30012018",
"Factors":{"Drug treatment":"Lumefantrine-30012018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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"Factors":{"Drug treatment":"Mefloquine-30012018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MethyleneBlue-18012018",
"Factors":{"Drug treatment":"MethyleneBlue-18012018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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"Factors":{"Drug treatment":"MMV000442-18102017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV000787-22092017",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV007181-05102017",
"Factors":{"Drug treatment":"MMV007181-05102017"},
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV007181-22092017",
"Factors":{"Drug treatment":"MMV007181-22092017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV019555-04072018",
"Factors":{"Drug treatment":"MMV019555-04072018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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"Factors":{"Drug treatment":"MMV019555-26072017"},
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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"Factors":{"Drug treatment":"MMV020746-21062017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV020746-22092017",
"Factors":{"Drug treatment":"MMV020746-22092017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV021735-11102018",
"Factors":{"Drug treatment":"MMV021735-11102018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV022224-11102018",
"Factors":{"Drug treatment":"MMV022224-11102018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV022478-11022019",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV027496-11102018",
"Factors":{"Drug treatment":"MMV027496-11102018"},
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV030666-11102018",
"Factors":{"Drug treatment":"MMV030666-11102018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV085071-04072018",
"Factors":{"Drug treatment":"MMV085071-04072018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV665794-16032017",
"Factors":{"Drug treatment":"MMV665794-16032017"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"MMV665939-21062017",
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"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"10xIC50"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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},
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"Naphthoquine-30012018",
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},
{
"Subject ID":"3x Technical Replicates of Process Blanks",
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"Additional sample data":{"Data presented":"raw peak area","Duration":"-","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of Process Blanks",
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},
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"Subject ID":"3x Technical Replicates of Process Blanks",
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"Additional sample data":{"Data presented":"raw peak area","Duration":"-","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of Process Blanks",
"Sample ID":"Blank-11022019",
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},
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"Subject ID":"3x Technical Replicates of Process Blanks",
"Sample ID":"Blank-11102018",
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},
{
"Subject ID":"3x Technical Replicates of Process Blanks",
"Sample ID":"Blank-16032017",
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},
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"Subject ID":"3x Technical Replicates of Process Blanks",
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},
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"Subject ID":"3x Technical Replicates of Process Blanks",
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"Additional sample data":{"Data presented":"raw peak area","Duration":"-","Amount":"-"}
},
{
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"Factors":{"Drug treatment":"No treatment"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"-","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of Process Blanks",
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},
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"Subject ID":"3x Technical Replicates of Process Blanks",
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},
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"Additional sample data":{"Data presented":"raw peak area","Duration":"-","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of Process Blanks",
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"Additional sample data":{"Data presented":"raw peak area","Duration":"-","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"Pipquine-18012018",
"Factors":{"Drug treatment":"Pipquine-18012018"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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},
{
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},
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-11022019",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-11102018",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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},
{
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-18102017",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-21062017",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-26072017",
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},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-27062018",
"Factors":{"Drug treatment":"Treated with no drug"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-29062017",
"Factors":{"Drug treatment":"Treated with no drug"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"ND-30012018",
"Factors":{"Drug treatment":"Treated with no drug"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"-"}
},
{
"Subject ID":"3x Technical Replicates of 1x10^8 MACS seperated trophozoite-infected cells",
"Sample ID":"WLL-11022019",
"Factors":{"Drug treatment":"WLL-11022019"},
"Additional sample data":{"Data presented":"raw peak area","Duration":"2.5 hours","Amount":"-"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes","SAMPLE_TYPE":"Cultured cells","COLLECTION_METHOD":"Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes","COLLECTION_LOCATION":"Biological safety hood","COLLECTION_FREQUENCY":"once after 2.5 hours treatment","COLLECTION_DURATION":"Collection and extraction occurs in under 20 minutes per plate","VOLUMEORAMOUNT_COLLECTED":"1 mL containing 1x10^8 infected cells","STORAGE_CONDITIONS":"On ice","COLLECTION_VIALS":"1.5 mL eppendorf","STORAGE_VIALS":"1.5 mL eppendorf","TISSUE_CELL_QUANTITY_TAKEN":"1 mL containing 1x10^8 infected cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Infected Red Blood cells were exposed to Antimalarial Compounds, associated with sample names. No treatment (as in the case of blanks) denotes these samples did not undergo the treatment incubation (blanks are made at the point of extraction in this case), whereas treated with no drug relates that these samples (no drug or ND) underwent the same treatment incubation as other treated samples, but in this case as a negative control with no drug administered.","TREATMENT":"Abiotic","TREATMENT_COMPOUND":"Atovaquone, Dihydroartemisinin (DHA), Ferroquin (FQ), GNF-Pf-5660, KAI407, Lumefantrine (LMF), Methylene Blue, MMV00017 (Naphthoquine), MMV000442, MMV00787, MMV007181, MMV019555, MMV020746, MMV021735, MMV022224, MMV022478, MMV027496, MMV030666, MMV085071, MMV665794, MMV665939, MMV667491, MMV668311, MMV675939, Mefloquine (MQ), Piperaquine (PPQ), WLL","TREATMENT_ROUTE":"Addition to media","TREATMENT_DOSE":"10xIC50","TREATMENT_DOSEVOLUME":"Always less than 10 uL per 5 mL sample","TREATMENT_DOSEDURATION":"2.5 hours","TREATMENT_VEHICLE":"Stocks kept in either DMSO or Water","CELL_STORAGE":"Temperature/Gas Mixture controlled incubator","CELL_GROWTH_CONTAINER":"6-well plate","CELL_GROWTH_CONFIG":"5 mL per well, each with 1x10^8 cells","CELL_MEDIA":"RPMI 1640 w/ Albumax, Gentamycin, Hypoxanthine, HEPES, Sodium Bicarbonate","CELL_HARVESTING":"PBS Wash followed by 90% methanol extraction"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples washed in PBS, spun down, aspirated, extracted in 90% methanol with labelled aspartate, then dried, resuspended in water labelled with chlorpropamide","SAMPLEPREP_PROTOCOL_FILENAME":"Metabolite_Extraction_for_LCMS_2017_Llinas.pdf","PROCESSING_METHOD":"Wash, Lysis, Drying, resuspension","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"90% Methanol Lysis","EXTRACT_CLEANUP":"Centrifugation, pellet removal","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"100 uL water with chlorpropamide","SAMPLE_SPIKING":"Labelled Aspartate, Chlorpropamide"},

"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"XSelect T3 XP Column Reversed-Phase 2.5 µm Spherical Silica (2.1 mm x 100 mm)","CHROMATOGRAPHY_TYPE":"Reversed phase"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"Blank subtraction, RSD cutoffs both by RSD per sample and pooled QCs to eliminate metabolites affected by time-dependency","ION_MODE":"NEGATIVE"},

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

"Data":[{"Metabolite":"1_3-Bisphosphoglyceric 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