{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001664","ANALYSIS_ID":"AN002716","VERSION":"1","CREATED_ON":"January 28, 2021, 11:02 am"},

"PROJECT":{"PROJECT_TITLE":"Effect of IPL on E.coli Metabolome amino acids","PROJECT_TYPE":"Untargeted LC-MS metabolomic study","PROJECT_SUMMARY":"Intense pulsed light (IPL) is becoming a new technical platform for disinfecting food against pathogenic bacteria. Metabolic changes are deemed to occur in bacteria as either the causes or the consequences of IPL-elicited bactericidal and bacteriostatic effects. However, little is known about the influences of IPL on bacterial metabolome. In this study, the IPL treatment was applied to E. coli K-12 for 0-20s, leading to time- and dose-dependent reductions in colony-forming units (CFU) and morphological changes. Cytoplasmic metabolites of the control and IPL-treated E. coli were examined by the liquid chromatography-mass spectrom-etry (LC-MS)-based metabolomic fingerprinting. The results from multivariate modeling and marker identification indicated that the metabolites in redox response, glycolysis, amino acid and nucleotide metabolism were selectively affected by the IPL treatments.","INSTITUTE":"University of Minnesota","LAST_NAME":"Chen","FIRST_NAME":"Chi","ADDRESS":"1334 Eckles Ave, St Paul, Minnesota, 55108, USA","EMAIL":"chichen@umn.edu","PHONE":"6126247704"},

"STUDY":{"STUDY_TITLE":"E.coli K-12 treated by IPL - analysis of polar phase (part-II)","STUDY_SUMMARY":"E.coli K-12 cells were treated by IPL, extracted and separated into organic/lipid phase and polar phase. Chemical derivatization with dansyl chloride was applied for analysis of amino acids in the polar phase extraction.","INSTITUTE":"University of Minnesota","LAST_NAME":"Chen","FIRST_NAME":"Chi","ADDRESS":"1334 Eckles Ave, St Paul, Minnesota, 55108, USA","EMAIL":"chichen@umn.edu","PHONE":"6126247704"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"316407","SUBJECT_COMMENTS":"E. coli strain K-12 W3110"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"ctl_1",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_ctl_1"}
},
{
"Subject ID":"-",
"Sample ID":"ctl_2",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_ctl_2"}
},
{
"Subject ID":"-",
"Sample ID":"ctl_3",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_ctl_3"}
},
{
"Subject ID":"-",
"Sample ID":"ctl_4",
"Factors":{"Treatment":"control"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_ctl_4"}
},
{
"Subject ID":"-",
"Sample ID":"5s_1",
"Factors":{"Treatment":"IPL 5 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_5s_1"}
},
{
"Subject ID":"-",
"Sample ID":"5s_2",
"Factors":{"Treatment":"IPL 5 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_5s_2"}
},
{
"Subject ID":"-",
"Sample ID":"5s_3",
"Factors":{"Treatment":"IPL 5 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_5s_3"}
},
{
"Subject ID":"-",
"Sample ID":"5s_4",
"Factors":{"Treatment":"IPL 5 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_5s_4"}
},
{
"Subject ID":"-",
"Sample ID":"10s_1",
"Factors":{"Treatment":"IPL 10 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_10s_1"}
},
{
"Subject ID":"-",
"Sample ID":"10s_2",
"Factors":{"Treatment":"IPL 10 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_10s_2"}
},
{
"Subject ID":"-",
"Sample ID":"10s_3",
"Factors":{"Treatment":"IPL 10 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_10s_3"}
},
{
"Subject ID":"-",
"Sample ID":"10s_4",
"Factors":{"Treatment":"IPL 10 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_10s_4"}
},
{
"Subject ID":"-",
"Sample ID":"15s_1",
"Factors":{"Treatment":"IPL 15 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_15s_1"}
},
{
"Subject ID":"-",
"Sample ID":"15s_2",
"Factors":{"Treatment":"IPL 15 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_15s_2"}
},
{
"Subject ID":"-",
"Sample ID":"15s_3",
"Factors":{"Treatment":"IPL 15 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_15s_3"}
},
{
"Subject ID":"-",
"Sample ID":"15s_4",
"Factors":{"Treatment":"IPL 15 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_15s_4"}
},
{
"Subject ID":"-",
"Sample ID":"20s_1",
"Factors":{"Treatment":"IPL 20 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_20s_1"}
},
{
"Subject ID":"-",
"Sample ID":"20s_2",
"Factors":{"Treatment":"IPL 20 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_20s_2"}
},
{
"Subject ID":"-",
"Sample ID":"20s_3",
"Factors":{"Treatment":"IPL 20 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_20s_3"}
},
{
"Subject ID":"-",
"Sample ID":"20s_4",
"Factors":{"Treatment":"IPL 20 s"},
"Additional sample data":{"RAW_FILE_NAME":"180312_QM_ecoli_extraction_polar phase_20s_4"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"E.coli strain K-12 was cultured in LB broth and harvested at OD=1. After centrifuge, cell pellets were harvested and washed with PBS twice. Then the pellet was re-suspended in PBS for further treatment.","COLLECTION_PROTOCOL_FILENAME":"Cell_culture_IPL treatment_Sample preparation_method.docx","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"For each IPL treatment, a 30 mL K-12 suspension in PBS was loaded in a petri dish (15 cm diameter) and then placed under the broad-spectrum light (wavelength 190-1100 nm) in a Z-1000 SteriPulse-XL system (Xenon Corporation, Woburn, MA). The samples were treated with the IPL for 0, 5, 10, 15, and 20 s.","TREATMENT_PROTOCOL_FILENAME":"Cell_culture_IPL treatment_Sample preparation_method.docx"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The control and IPL-treated E. coli samples were centrifuged for obtaining the pellets, which were then washed with PBS twice. After extraction with methanol-water-chloroform, the polar phase was separated and derivatized with dansyl chloride (DC) for amino acid analysis.","SAMPLEPREP_PROTOCOL_FILENAME":"Cell_culture_IPL treatment_Sample preparation_method.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um)"},

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

"MS":{"INSTRUMENT_NAME":"Waters Xevo-G2-S","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Features were captured by MarkerLynx (Waters) and processed. The relative intensity of each ion was calculated by normalizing the single ion counts (SIC) versus the total ion counts (TIC) in the whole chromatogram, while setting the TIC arbitrarily to 10,000.","MS_RESULTS_FILE":"ST001664_AN002716_Results.txt UNITS:no applicable unites Has m/z:Yes Has RT:Yes RT units:Minutes"}

}