#METABOLOMICS WORKBENCH jaredmayers_20240429_191454 DATATRACK_ID:4801 STUDY_ID:ST003187 ANALYSIS_ID:AN005235 PROJECT_ID:PR001807 VERSION 1 CREATED_ON April 30, 2024, 6:43 am #PROJECT PR:PROJECT_TITLE A metabolomics pipeline highlights microbial metabolism in bloodstream PR:PROJECT_TITLE infections - untargeted metabolomics on bacterial cell culture supernatants PR:PROJECT_SUMMARY Untargeted metabolomics on bacterial cell culture supernatants after overnight PR:PROJECT_SUMMARY culture PR:INSTITUTE Harvard University PR:LAST_NAME Mayers PR:FIRST_NAME Jared PR:ADDRESS 12 Oxford St Conant 200S, Cambridge, MA, 02138, USA PR:EMAIL jrmayers@gmail.com PR:PHONE 4259417747 #STUDY ST:STUDY_TITLE Untargeted plasma metabolomics on bacterial culture supernatants ST:STUDY_SUMMARY As part of our pipeline to identify microbial metabolites in bloodstream ST:STUDY_SUMMARY infections, we performed untargeted metabolomics on bacterial cell culture ST:STUDY_SUMMARY supernatants. We focused on metabolites that were significantly altered in both ST:STUDY_SUMMARY our human cohort (PR001807) and mouse model of bloodstream infection ST:INSTITUTE Harvard University ST:LAST_NAME Mayers ST:FIRST_NAME Jared ST:ADDRESS 12 Oxford St Conant 200S Cambridge, MA 02138 ST:EMAIL jrmayers@gmail.com ST:PHONE 4259417747 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Escherichia coli SU:TAXONOMY_ID 562 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - CFT073_LB Factor:LB_cells | Sample source:media RAW_FILE_NAME(File Name)=CFT073_LB SUBJECT_SAMPLE_FACTORS - K12_LB Factor:LB_cells | Sample source:media RAW_FILE_NAME(File Name)=K12_LB SUBJECT_SAMPLE_FACTORS - K12_M9 Factor:M9_cells | Sample source:media RAW_FILE_NAME(File Name)=K12_M9 SUBJECT_SAMPLE_FACTORS - KEIO_LB Factor:LB_cells | Sample source:media RAW_FILE_NAME(File Name)=KEIO_LB SUBJECT_SAMPLE_FACTORS - KEIO_M9 Factor:M9_cells | Sample source:media RAW_FILE_NAME(File Name)=KEIO_M9 SUBJECT_SAMPLE_FACTORS - LB_blank Factor:LB_media | Sample source:media RAW_FILE_NAME(File Name)=LB_blank SUBJECT_SAMPLE_FACTORS - M9_blank Factor:M9_media | Sample source:media RAW_FILE_NAME(File Name)=M9_blank #COLLECTION CO:COLLECTION_SUMMARY Media supernatant from overnight cultures. After overnight growth, cells were CO:COLLECTION_SUMMARY pellet and media aspirated for extraction CO:SAMPLE_TYPE Media #TREATMENT TR:TREATMENT_SUMMARY Media blanks were aliquoted and incubated overnight at 37C. Cells were TR:TREATMENT_SUMMARY innoculated into designated media and grown overnight for 16hrs at 37C before TR:TREATMENT_SUMMARY harvesting #SAMPLEPREP SP:SAMPLEPREP_SUMMARY 1 part media with 9 parts 75:25:0.2 ACN:MetOH:Formic Acid with internal val-d8 SP:SAMPLEPREP_SUMMARY and phe-d8 standards; vortexed, centrifuged, supernatant removed and run on SP:SAMPLEPREP_SUMMARY LC-MS #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 Infinity HPLC CH:COLUMN_NAME Waters Atlantis HILIC (150 x 2.1mm,3um) CH:SOLVENT_A 100% water; 0.1% formic acid CH:SOLVENT_B 100% acetonitrile; 0.1% formic acid CH:FLOW_GRADIENT 0.5 minute at 5% mobile phase B followed by a linear gradient to 40% mobile CH:FLOW_GRADIENT phase B over 10 minutes CH:FLOW_RATE 250 μL/min CH:COLUMN_TEMPERATURE 30 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Raw data from the LC–MS were analyzed using Agilent MassHunter Qualitative MS:MS_COMMENTS Analysis 10.0 software. MS:MS_RESULTS_FILE ST003187_AN005235_Results.txt UNITS:ion counts Has m/z:Yes Has RT:Yes RT units:Minutes #END