#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