{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000262","ANALYSIS_ID":"AN000417","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"FLUTE: Functionalizing Lists of Unknown TB Entities","PROJECT_TYPE":"NIH U19","PROJECT_SUMMARY":"functional genomics of proteins of unknown function in M. tuberculosis","INSTITUTE":"Weill Cornell Medical College","DEPARTMENT":"Microbiology and Immunology","LAST_NAME":"Rhee","FIRST_NAME":"Kyu","ADDRESS":"#N/A","EMAIL":"kyr9001@med.cornell.edu","PHONE":"-"},

"STUDY":{"STUDY_TITLE":"Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1713","STUDY_TYPE":"timecourse","STUDY_SUMMARY":"These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might","INSTITUTE":"Weill Cornell Medical College","DEPARTMENT":"Microbiology and Immunology","LAST_NAME":"Rhee","FIRST_NAME":"Kyu","ADDRESS":"Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY","EMAIL":"kyr9001@med.cornell.edu","PHONE":"-","NUM_GROUPS":"3 replicates X 3 timepoints X with/without GTP","STUDY_COMMENTS":"The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor."},

"SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Mycobacterium tuberculosis H37Rv","TAXONOMY_ID":"83332","GENOTYPE_STRAIN":"Mycobacterium tuberculosis H37Rv, taxid:","SPECIES_GROUP":"Microorganism"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_A_0",
"Factors":{"timepoint (min)":"0","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_A_0",
"Factors":{"timepoint (min)":"0","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_A_15",
"Factors":{"timepoint (min)":"15","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_A_15",
"Factors":{"timepoint (min)":"15","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_A_30",
"Factors":{"timepoint (min)":"30","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_A_30",
"Factors":{"timepoint (min)":"30","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_B_0",
"Factors":{"timepoint (min)":"0","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_B_0",
"Factors":{"timepoint (min)":"0","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_B_15",
"Factors":{"timepoint (min)":"15","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_B_15",
"Factors":{"timepoint (min)":"15","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_B_30",
"Factors":{"timepoint (min)":"30","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_B_30",
"Factors":{"timepoint (min)":"30","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_C_0",
"Factors":{"timepoint (min)":"0","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_C_0",
"Factors":{"timepoint (min)":"0","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_C_15",
"Factors":{"timepoint (min)":"15","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_C_15",
"Factors":{"timepoint (min)":"15","co-factor added to lysate":"None"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1mMGTP1713_C_30",
"Factors":{"timepoint (min)":"30","co-factor added to lysate":"1mM GTP"}
},
{
"Subject ID":"Rv1713",
"Sample ID":"1713_C_30",
"Factors":{"timepoint (min)":"30","co-factor added to lysate":"None"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"protein expression","COLLECTION_PROTOCOL_ID":"Rv1713 from M. tuberculosis H37Rv was expressed in E. coli cells and purified...","COLLECTION_VIALS":"polypropylene microfuge tubes","STORAGE_VIALS":"Agilent polypropylene conical bottom vials"},

"TREATMENT":{"TREATMENT_SUMMARY":"-"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"10 uM enzyme incubated at 25C in M. bovis whole-cell extract","PROCESSING_METHOD":"extract was lyophilized and resuspended in 20 mM Tris-HCL pH 8.0","PROCESSING_STORAGE_CONDITIONS":"cell pellet frozen at -80C","EXTRACTION_METHOD":"70% acetonitrile","EXTRACT_CLEANUP":"centrifugation followed by aspiration of supernatant and lyophilization","EXTRACT_STORAGE":"frozen at -80C"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Aqueous normal phase diamond hydride","CHROMATOGRAPHY_TYPE":"Normal phase","INSTRUMENT_NAME":"Agilent 1290","COLUMN_NAME":"Microsolv Diamond hydride (150mm, 4um)","METHODS_FILENAME":"ANPpos/ANP_neg","FLOW_RATE":"0.4 ml/min","SOLVENT_A":"H20 +0.2% formic acid","SOLVENT_B":"acetonitrile + 0.2% formic acid","ANALYTICAL_TIME":"24 minutes","WASHING_BUFFER":"50% methanol"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Rhee Lab","SOFTWARE_VERSION":"XCMS online","DETECTOR_TYPE":"Agilent 6220 ToF MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6220 TOF","INSTRUMENT_TYPE":"TOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_VOLTAGE":"3500","DRY_GAS_FLOW":"10 l/min","DRY_GAS_TEMP":"250","FRAGMENT_VOLTAGE":"135V","MASS_ACCURACY":"5 ppm","NEBULIZER":"35","OCTPOLE_VOLTAGE":"400","SCAN_RANGE_MOVERZ":"50-1200","SCANNING_CYCLE":"1.4","SKIMMER_VOLTAGE":"65","MS_COMMENTS":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"integrated peak counts",

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