{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002078","ANALYSIS_ID":"AN003390","VERSION":"1","CREATED_ON":"January 25, 2022, 10:36 am"},

"PROJECT":{"PROJECT_TITLE":"Multiple modes of interfering with the activity of Plasmodium falciparum cytoplasmic isoleucyl-tRNA synthetase illustrate the enzyme is a promising antimalarial target.","PROJECT_SUMMARY":"Here we interrogated the in vitro metabolic effects of 6 drugs using ultra-high performance liquid chromatography mass-spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention. We interrogate the metabolic effects on the 3D7 parasite strain. The metabolic effects were compared to their parent strain. The metabolic fingerprints provided show that certain biochemical pathways are affected by the drug inhibitory effect.","INSTITUTE":"Pennsylvania State University","DEPARTMENT":"Department of Biochemistry and Molecular Biology","LAST_NAME":"Llinas","FIRST_NAME":"Manuel","ADDRESS":"W126 Millenium Science Complex, University Park, PA 16802","EMAIL":"manuel@psu.edu","PHONE":"814-867-3527"},

"STUDY":{"STUDY_TITLE":"Multiple modes of interfering with the activity of Plasmodium falciparum cytoplasmic isoleucyl-tRNA synthetase illustrate the enzyme is a promising antimalarial target.","STUDY_SUMMARY":"Here we interrogated the in vitro metabolic effects of 6 drugs using ultra-high performance liquid chromatography mass-spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention. We interrogate the metabolic effects on the 3D7 parasite strain. The metabolic effects were compared to their parent strain. The metabolic fingerprints provided show that certain biochemical pathways are affected by the drug inhibitory effect.","INSTITUTE":"Pennsylvania State University","DEPARTMENT":"Department of Biochemistry and Molecular Biology","LAST_NAME":"Llinas","FIRST_NAME":"Manuel","ADDRESS":"W126 Millenium Science Complex, University Park, PA 16802","EMAIL":"manuel@psu.edu","PHONE":"814-867-3527"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Plasmodium falciparum","TAXONOMY_ID":"5833","GENOTYPE_STRAIN":"3D7"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"MMV1091186_1",
"Factors":{"Drug":"MMV1091186"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1091186_1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1091186_2",
"Factors":{"Drug":"MMV1091186"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1091186_2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1091186_3",
"Factors":{"Drug":"MMV1091186"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1091186_3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1081413_1",
"Factors":{"Drug":"MMV1081413"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1081413_1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1081413_2",
"Factors":{"Drug":"MMV1081413"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1081413_2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1081413_3",
"Factors":{"Drug":"MMV1081413"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1081413_3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Halofuginone1",
"Factors":{"Drug":"Halofuginone"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Halofuginone1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Halofuginone2",
"Factors":{"Drug":"Halofuginone"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Halofuginone2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Halofuginone3",
"Factors":{"Drug":"Halofuginone"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Halofuginone3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1578884_1",
"Factors":{"Drug":"MMV1578884"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1578884_1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1578884_2",
"Factors":{"Drug":"MMV1578884"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1578884_2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"MMV1578884_3",
"Factors":{"Drug":"MMV1578884"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"MMV1578884_3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OSM-S-106-1",
"Factors":{"Drug":"OSM-S-106"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"OSM-S-106-1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OSM-S-106-2",
"Factors":{"Drug":"OSM-S-106"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"OSM-S-106-2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OSM-S-106-3",
"Factors":{"Drug":"OSM-S-106"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"OSM-S-106-3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"TCMDC-124553-1",
"Factors":{"Drug":"TCMDC-124553"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"TCMDC-124553-1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"TCMDC-124553-2",
"Factors":{"Drug":"TCMDC-124553"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"TCMDC-124553-2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"TCMDC-124553-3",
"Factors":{"Drug":"TCMDC-124553"},
"Additional sample data":{"Concentration":"10X IC50","Treatment time":"2.5 hours","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"TCMDC-124553-3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"ND1",
"Factors":{"Drug":"ND"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"ND1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"ND2",
"Factors":{"Drug":"ND"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"ND2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"ND3",
"Factors":{"Drug":"ND"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"ND3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Pool1",
"Factors":{"Drug":"Pool"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Pool1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Pool2",
"Factors":{"Drug":"Pool"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Pool2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Pool3",
"Factors":{"Drug":"Pool"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Pool3.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Blank1",
"Factors":{"Drug":"Blank"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Blank1.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Blank2",
"Factors":{"Drug":"Blank"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Blank2.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"Blank3",
"Factors":{"Drug":"Blank"},
"Additional sample data":{"Concentration":"N/A","Treatment time":"N/A","Parasite Stage":"MACS purified Troph","RAW_FILE_NAME":"Blank3.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were pelleted and the media aspirated prior to extraction","SAMPLE_TYPE":"Pf infected RBCs"},

"TREATMENT":{"TREATMENT_SUMMARY":"Purified iRBCs were treated with 10XIC50 drug for 2.5 hours"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"90% Methanol/10% water at 50:1 solvent/cell pellet followed by vortexing and clarification via centrifugation","PROCESSING_METHOD":"Lysis","PROCESSING_STORAGE_CONDITIONS":"4℃","EXTRACTION_METHOD":"See SA Cobbold et al JBC 2013","EXTRACT_CLEANUP":"Clarification via centrifugation followed by nitrogen drying","EXTRACT_STORAGE":"-80℃","SAMPLE_SPIKING":"Internal Standard 13C4, 15N1-Aspartate used for sample preparation normalizer"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"Water XSelect HSS T3 C18 (100 x 2.1mm, 2.5um)","INTERNAL_STANDARD":"13C4, 15N1-Aspartate","PRECONDITIONING":"Water Blanks"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"El-Maven was used to process converted .mzXML"},

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

"Data":[{"Metabolite":"aspartate (standard)","ND1":"3.47E+08","ND2":"3.55E+08","ND3":"3.51E+08","Pool1":"4.04E+08","Pool2":"3.53E+08","Pool3":"2.61E+08","TCMDC-124553-1":"3.29E+08","TCMDC-124553-2":"3.15E+08","TCMDC-124553-3":"2.88E+08","Blank2":"3.77E+08","Blank3":"2.94E+08"},{"Metabolite":"chlorpropamide","ND1":"2.29E+09","ND2":"2.28E+09","ND3":"2.33E+09","Pool1":"2.76E+09","Pool2":"2.30E+09","Pool3":"1.71E+09","TCMDC-124553-1":"2.32E+09","TCMDC-124553-2":"2.16E+09","TCMDC-124553-3":"1.90E+09","Blank2":"2.11E+09","Blank3":"1.69E+09"},{"Metabolite":"pyruvate","ND1":"3.51E+08","ND2":"3.49E+08","ND3":"3.92E+08","Pool1":"3.93E+08","Pool2":"3.28E+08","Pool3":"2.11E+08","TCMDC-124553-1":"2.81E+08","TCMDC-124553-2":"2.93E+08","TCMDC-124553-3":"4.83E+08","Blank2":"5548898","Blank3":"2.01E+07"},{"Metabolite":"alanine/sarcosine","ND1":"1.99E+07","ND2":"2.44E+07","ND3":"2.47E+07","Pool1":"2.06E+07","Pool2":"1.84E+07","Pool3":"1.57E+07","TCMDC-124553-1":"1.85E+07","TCMDC-124553-2":"1.73E+07","TCMDC-124553-3":"2.20E+07","Blank2":"564389.6","Blank3":"4686302"},{"Metabolite":"lactate","ND1":"2.57E+09","ND2":"3.30E+09","ND3":"3.28E+09","Pool1":"3.39E+09","Pool2":"2.88E+09","Pool3":"2.47E+09","TCMDC-124553-1":"1.62E+09","TCMDC-124553-2":"2.49E+09","TCMDC-124553-3":"3.89E+09","Blank2":"2.70E+08","Blank3":"1.86E+09"},{"Metabolite":"4-aminobutyrate","ND1":"1.19E+08","ND2":"1.22E+08","ND3":"1.24E+08","Pool1":"1.26E+08","Pool2":"1.06E+08","Pool3":"8.44E+07","TCMDC-124553-1":"1.07E+08","TCMDC-124553-2":"9.72E+07","TCMDC-124553-3":"8.94E+07","Blank2":"36845.77","Blank3":"34848.38"},{"Metabolite":"serine","ND1":"5.10E+07","ND2":"5.62E+07","ND3":"5.35E+07","Pool1":"5.51E+07","Pool2":"4.99E+07","Pool3":"4.15E+07","TCMDC-124553-1":"5.08E+07","TCMDC-124553-2":"5.31E+07","TCMDC-124553-3":"4.62E+07","Blank2":"2580979","Blank3":"3.35E+07"},{"Metabolite":"proline","ND1":"8.77E+07","ND2":"8.88E+07","ND3":"9.30E+07","Pool1":"8.94E+07","Pool2":"8.24E+07","Pool3":"6.87E+07","TCMDC-124553-1":"7.82E+07","TCMDC-124553-2":"8.04E+07","TCMDC-124553-3":"1.02E+08","Blank2":"468833.8","Blank3":"4938639"},{"Metabolite":"fumarate","ND1":"6.96E+07","ND2":"7.14E+07","ND3":"7.48E+07","Pool1":"5.80E+07","Pool2":"4.49E+07","Pool3":"3.42E+07","TCMDC-124553-1":"5.02E+07","TCMDC-124553-2":"4.22E+07","TCMDC-124553-3":"4.43E+07","Blank2":"556669.6","Blank3":"612384"},{"Metabolite":"maleic acid","ND1":"2.79E+08","ND2":"2.62E+08","ND3":"2.93E+08","Pool1":"1.90E+08","Pool2":"1.79E+08","Pool3":"1.49E+08","TCMDC-124553-1":"1.53E+08","TCMDC-124553-2":"1.61E+08","TCMDC-124553-3":"1.65E+08","Blank2":"3076930.6","Blank3":"5222050"},{"Metabolite":"valine","ND1":"5.98E+08","ND2":"5.31E+08","ND3":"5.65E+08","Pool1":"5.11E+08","Pool2":"4.54E+08","Pool3":"3.51E+08","TCMDC-124553-1":"4.51E+08","TCMDC-124553-2":"4.86E+08","TCMDC-124553-3":"4.90E+08","Blank2":"5965549","Blank3":"1.14E+07"},{"Metabolite":"succinate/Methylmalonic acid","ND1":"1.05E+09","ND2":"1.06E+09","ND3":"1.10E+09","Pool1":"1.19E+09","Pool2":"9.69E+08","Pool3":"7.42E+08","TCMDC-124553-1":"1.05E+09","TCMDC-124553-2":"8.96E+08","TCMDC-124553-3":"9.70E+08","Blank2":"7.74E+07","Blank3":"9.98E+07"},{"Metabolite":"threonine/homoserine","ND1":"8.16E+07","ND2":"9.27E+07","ND3":"8.14E+07","Pool1":"7.58E+07","Pool2":"6.39E+07","Pool3":"5.49E+07","TCMDC-124553-1":"7.81E+07","TCMDC-124553-2":"7.25E+07","TCMDC-124553-3":"6.66E+07","Blank2":"1180488","Blank3":"8886788"},{"Metabolite":"nicotinate","ND1":"1.59E+07","ND2":"1.58E+07","ND3":"1.69E+07","Pool1":"2.14E+07","Pool2":"1.91E+07","Pool3":"1.48E+07","TCMDC-124553-1":"1.45E+07","TCMDC-124553-2":"1.51E+07","TCMDC-124553-3":"2.15E+07","Blank2":"16732.25","Blank3":"15212.36"},{"Metabolite":"DL-Pipecolic 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}

}