#METABOLOMICS WORKBENCH U19-Rv1713-AMBP-MWB-metadata.xlsx DATATRACK_ID:421 STUDY_ID:ST000262 ANALYSIS_ID:AN000418 VERSION 1 CREATED_ON 02-08-2024 #PROJECT PR:PROJECT_TITLE FLUTE: Functionalizing Lists of Unknown TB Entities PR:PROJECT_TYPE NIH U19 PR:PROJECT_SUMMARY functional genomics of proteins of unknown function in M. tuberculosis PR:INSTITUTE Weill Cornell Medicine PR:DEPARTMENT Microbiology and Immunology PR:LAST_NAME Rhee PR:FIRST_NAME Kyu PR:ADDRESS #N/A PR:EMAIL kyr9001@med.cornell.edu PR:DOI http://dx.doi.org/10.21228/M8388M #STUDY ST:STUDY_TITLE Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1713 ST:STUDY_TYPE timecourse ST:STUDY_SUMMARY These experiments involve incubating various proteins of unknown function in the ST:STUDY_SUMMARY M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite ST:STUDY_SUMMARY levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might ST:STUDY_SUMMARY catalyze. ST:INSTITUTE Weill Cornell Medicine ST:DEPARTMENT Microbiology and Immunology ST:LAST_NAME Rhee ST:FIRST_NAME Kyu ST:ADDRESS Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 ST:ADDRESS York Avenue, New York, NY ST:EMAIL kyr9001@med.cornell.edu ST:SUBMIT_DATE 2015-11-13 #SUBJECT SU:SUBJECT_TYPE Bacterial cells SU:SUBJECT_SPECIES Mycobacterium tuberculosis H37Rv SU:TAXONOMY_ID 83332 SU:GENOTYPE_STRAIN Mycobacterium tuberculosis H37Rv, taxid: SU:SPECIES_GROUP Microorganism #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_A_0 timepoint (min):0 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_B_0 timepoint (min):0 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_C_0 timepoint (min):0 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1713_A_0 timepoint (min):0 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1713_B_0 timepoint (min):0 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1713_C_0 timepoint (min):0 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_A_15 timepoint (min):15 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_B_15 timepoint (min):15 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_C_15 timepoint (min):15 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1713_A_15 timepoint (min):15 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1713_B_15 timepoint (min):15 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1713_C_15 timepoint (min):15 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_A_30 timepoint (min):30 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_B_30 timepoint (min):30 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1mMGTP1713_C_30 timepoint (min):30 | co-factor added to lysate:1mM GTP SUBJECT_SAMPLE_FACTORS Rv1713 1713_A_30 timepoint (min):30 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1713_B_30 timepoint (min):30 | co-factor added to lysate:None SUBJECT_SAMPLE_FACTORS Rv1713 1713_C_30 timepoint (min):30 | co-factor added to lysate:None #COLLECTION CO:COLLECTION_SUMMARY protein expression CO:COLLECTION_PROTOCOL_ID Rv1713 from M. tuberculosis H37Rv was expressed in E. coli cells and purified... CO:SAMPLE_TYPE Bacterial cells CO:COLLECTION_VIALS polypropylene microfuge tubes CO:STORAGE_VIALS Agilent polypropylene conical bottom vials #TREATMENT #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 10 uM enzyme incubated at 25C in M. bovis whole-cell extract SP:PROCESSING_METHOD extract was lyophilized and resuspended in 20 mM Tris-HCL pH 8.0 SP:PROCESSING_STORAGE_CONDITIONS cell pellet frozen at -80C SP:EXTRACTION_METHOD 70% acetonitrile SP:EXTRACT_CLEANUP centrifugation followed by aspiration of supernatant and lyophilization SP:EXTRACT_STORAGE frozen at -80C #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Aqueous normal phase diamond hydride CH:METHODS_FILENAME ANPpos/ANP_neg CH:INSTRUMENT_NAME Agilent 1290 CH:COLUMN_NAME Microsolv Diamond hydride (150mm,4um) CH:FLOW_RATE 0.4 ml/min CH:SOLVENT_A 100% water; 0.2% formic acid CH:SOLVENT_B 100% acetonitrile; 0.2% formic acid CH:ANALYTICAL_TIME 24 minutes CH:WASHING_BUFFER 50% methanol CH:CHROMATOGRAPHY_TYPE Normal phase #ANALYSIS AN:LABORATORY_NAME Rhee Lab AN:ANALYSIS_TYPE MS AN:ANALYSIS_COMMENTS NEGATIVE AN:SOFTWARE_VERSION XCMS online AN:PROCESSED_FILE Rv1713.xlsx AN:DETECTOR_TYPE Agilent 6220 ToF MS #MS MS:INSTRUMENT_NAME Agilent 6220 TOF MS:INSTRUMENT_TYPE TOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:CAPILLARY_VOLTAGE 3500 MS:DRY_GAS_FLOW 10 l/min MS:DRY_GAS_TEMP 250 MS:FRAGMENT_VOLTAGE 135V MS:MASS_ACCURACY 5 ppm MS:NEBULIZER 35 MS:OCTPOLE_VOLTAGE 400 MS:SCAN_RANGE_MOVERZ 50-1200 MS:SCANNING_CYCLE 1.4 MS:SKIMMER_VOLTAGE 65 #END