{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001657","ANALYSIS_ID":"AN002705","VERSION":"1","CREATED_ON":"January 21, 2021, 2:59 pm"}, "PROJECT":{"PROJECT_TITLE":"Effect of IPL on E.coli Metabolome","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 ap-plied to E. coli K-12 for 0-20s, leading to time- and dose-dependent changes in E.coli metabolome. We consider the degradation of membrane-bound quinone electron carriers as the trigger of dramatic metabolis shift in IPL-treated E.coli.","INSTITUTE":"University of Minnesota","DEPARTMENT":"Food Science and Nutrition","LABORATORY":"Nutritional Metabolomics","LAST_NAME":"Chen","FIRST_NAME":"Chi","ADDRESS":"1334 Eckles Ave W, St Paul, MN 55108","EMAIL":"chichen@umn.edu","PHONE":"612-624-7704"}, "STUDY":{"STUDY_TITLE":"E.coli K-12 treated by IPL_analysis of organic phase","STUDY_SUMMARY":"In this study, E.coli K-12 was treated by intense pulsed light (IPL) for 0-20 seconds. Then the organic/lipid phase of the cellular metabolome was extracted and submitted to untargeted LC-MS based metabolomic study.","INSTITUTE":"University of Minnesota","DEPARTMENT":"Food Science and Nutrition","LABORATORY":"Nutritional Metabolomics","LAST_NAME":"Chen","FIRST_NAME":"Chi","ADDRESS":"1334 Eckles Ave","EMAIL":"chichen@umn.edu","PHONE":"6126247704"}, "SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562","GENOTYPE_STRAIN":"K-12 W3110"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"ctl_1", "Factors":{"Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_ctl_1"} }, { "Subject ID":"-", "Sample ID":"ctl_2", "Factors":{"Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_ctl_2"} }, { "Subject ID":"-", "Sample ID":"ctl_3", "Factors":{"Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_ctl_3"} }, { "Subject ID":"-", "Sample ID":"ctl_4", "Factors":{"Treatment":"control"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_ctl_4"} }, { "Subject ID":"-", "Sample ID":"5s_1", "Factors":{"Treatment":"IPL 5 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_5s_1"} }, { "Subject ID":"-", "Sample ID":"5s_2", "Factors":{"Treatment":"IPL 5 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_5s_2"} }, { "Subject ID":"-", "Sample ID":"5s_3", "Factors":{"Treatment":"IPL 5 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_5s_3"} }, { "Subject ID":"-", "Sample ID":"5s_4", "Factors":{"Treatment":"IPL 5 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_5s_4"} }, { "Subject ID":"-", "Sample ID":"10s_1", "Factors":{"Treatment":"IPL 10 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_10s_1"} }, { "Subject ID":"-", "Sample ID":"10s_2", "Factors":{"Treatment":"IPL 10 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_10s_2"} }, { "Subject ID":"-", "Sample ID":"10s_3", "Factors":{"Treatment":"IPL 10 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_10s_3"} }, { "Subject ID":"-", "Sample ID":"10s_4", "Factors":{"Treatment":"IPL 10 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_10s_4"} }, { "Subject ID":"-", "Sample ID":"15s_1", "Factors":{"Treatment":"IPL 15 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_15s_1"} }, { "Subject ID":"-", "Sample ID":"15s_2", "Factors":{"Treatment":"IPL 15 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_15s_2"} }, { "Subject ID":"-", "Sample ID":"15s_3", "Factors":{"Treatment":"IPL 15 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_15s_3"} }, { "Subject ID":"-", "Sample ID":"15s_4", "Factors":{"Treatment":"IPL 15 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_15s_4"} }, { "Subject ID":"-", "Sample ID":"20s_1", "Factors":{"Treatment":"IPL 20 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_20s_1"} }, { "Subject ID":"-", "Sample ID":"20s_2", "Factors":{"Treatment":"IPL 20 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_20s_2"} }, { "Subject ID":"-", "Sample ID":"20s_3", "Factors":{"Treatment":"IPL 20 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_20s_3"} }, { "Subject ID":"-", "Sample ID":"20s_4", "Factors":{"Treatment":"IPL 20 s"}, "Additional sample data":{"RAW_FILE_NAME":"180309_QM_ecoli_extraction_non-polar phase_20s_4"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"E. coli strain K-12 W3110 (ATCC 27325) was cultured on TSA agar medium. A single bacterial colony was picked from TSA agar medium, and then used to inoculate Luria-Bertani broth (EMD Millipore, Billerica, MA). After being incubated at 37 °C for 12 h on a rotary shaker set to 200 rpm, E. coli cells were harvested at an optical density (OD600) of 1, and then centrifuged at 7,500 × g for 10 min in 50 mL centrifuge tubes. After decanting the supernatant, the pellet was washed with phosphate buffered saline (PBS), and then re-suspended to the volume of bacterial culture for further treatment and analysis.","COLLECTION_PROTOCOL_FILENAME":"Cell culture_IPL treatment_Sample preparation_method.docx","SAMPLE_TYPE":"Bacterial cells"}, "TREATMENT":{"TREATMENT_SUMMARY":"E.coli K-12 was treated by a customized IPL instrument for 0 - 20 seconds.","TREATMENT_PROTOCOL_FILENAME":"Cell culture_IPL treatment_Sample preparation_method.docx"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"After IPL treatment, the cells were centrifuged and washed with PBS twice. The pellets then went though methanol-water-chloroform extraction for obtaining the organic/non-polar phase.","SAMPLEPREP_PROTOCOL_FILENAME":"Cell culture_IPL treatment_Sample preparation_method.docx"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"analysis of lipids","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)","FLOW_RATE":"0.5 mL/min","SOLVENT_A":"40% aqueous ACN containing 0.1% formic acid and 10mM NH4OAc","SOLVENT_B":"methanol solution containing 0.1% formic acid and 10mM NH4OAc"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Waters Xevo-G2-S","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Ion features were captured by MakerLynx (Waters) after eliminating noises.","MS_RESULTS_FILE":"ST001657_AN002705_Results.txt UNITS:no applicable unites Has m/z:Yes Has RT:Yes RT units:Minutes"} }