{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003187","ANALYSIS_ID":"AN005235","VERSION":"1","CREATED_ON":"April 30, 2024, 6:43 am"},

"PROJECT":{"PROJECT_TITLE":"A metabolomics pipeline highlights microbial metabolism in bloodstream infections - untargeted metabolomics on bacterial cell culture supernatants","PROJECT_SUMMARY":"Untargeted metabolomics on bacterial cell culture supernatants after overnight culture","INSTITUTE":"Harvard University","LAST_NAME":"Mayers","FIRST_NAME":"Jared","ADDRESS":"12 Oxford St Conant 200S, Cambridge, MA, 02138, USA","EMAIL":"jrmayers@gmail.com","PHONE":"4259417747"},

"STUDY":{"STUDY_TITLE":"Untargeted plasma metabolomics on bacterial culture supernatants","STUDY_SUMMARY":"As part of our pipeline to identify microbial metabolites in bloodstream infections, we performed untargeted metabolomics on bacterial cell culture supernatants. We focused on metabolites that were significantly altered in both our human cohort (PR001807) and mouse model of bloodstream infection","INSTITUTE":"Harvard University","LAST_NAME":"Mayers","FIRST_NAME":"Jared","ADDRESS":"12 Oxford St Conant 200S Cambridge, MA 02138","EMAIL":"jrmayers@gmail.com","PHONE":"4259417747"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CFT073_LB",
"Factors":{"Factor":"LB_cells","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"CFT073_LB"}
},
{
"Subject ID":"-",
"Sample ID":"K12_LB",
"Factors":{"Factor":"LB_cells","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"K12_LB"}
},
{
"Subject ID":"-",
"Sample ID":"K12_M9",
"Factors":{"Factor":"M9_cells","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"K12_M9"}
},
{
"Subject ID":"-",
"Sample ID":"KEIO_LB",
"Factors":{"Factor":"LB_cells","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"KEIO_LB"}
},
{
"Subject ID":"-",
"Sample ID":"KEIO_M9",
"Factors":{"Factor":"M9_cells","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"KEIO_M9"}
},
{
"Subject ID":"-",
"Sample ID":"LB_blank",
"Factors":{"Factor":"LB_media","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"LB_blank"}
},
{
"Subject ID":"-",
"Sample ID":"M9_blank",
"Factors":{"Factor":"M9_media","Sample source":"media"},
"Additional sample data":{"RAW_FILE_NAME(File Name)":"M9_blank"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Media supernatant from overnight cultures. After overnight growth, cells were pellet and media aspirated for extraction","SAMPLE_TYPE":"Media"},

"TREATMENT":{"TREATMENT_SUMMARY":"Media blanks were aliquoted and incubated overnight at 37C. Cells were innoculated into designated media and grown overnight for 16hrs at 37C before harvesting"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1 part media with 9 parts 75:25:0.2 ACN:MetOH:Formic Acid with internal val-d8 and phe-d8 standards; vortexed, centrifuged, supernatant removed and run on LC-MS"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1260 Infinity HPLC","COLUMN_NAME":"Waters Atlantis HILIC (150 x 2.1mm,3um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"100% acetonitrile; 0.1% formic acid","FLOW_GRADIENT":"0.5 minute at 5% mobile phase B followed by a linear gradient to 40% mobile phase B over 10 minutes","FLOW_RATE":"250 μL/min","COLUMN_TEMPERATURE":"30"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6530 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Raw data from the LC–MS were analyzed using Agilent MassHunter Qualitative Analysis 10.0 software.","MS_RESULTS_FILE":"ST003187_AN005235_Results.txt UNITS:ion counts Has m/z:Yes Has RT:Yes RT units:Minutes"}

}