{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001370","ANALYSIS_ID":"AN002286","VERSION":"1","CREATED_ON":"May 5, 2020, 11:00 am"},

"PROJECT":{"PROJECT_TITLE":"Chemotaxonomic profiling of Canadian Alternaria populations using high resolution mass spectrometry","PROJECT_TYPE":"Alternaria metabolomics","PROJECT_SUMMARY":"Alternaria spp. occur as plant pathogens worldwide under field and storage conditions. They lead to food spoilage and also produce several classes of secondary metabolites that contaminate the food production chain. From a food safety perspective, the major challenge with assessing the risk of Alternaria contamination is the lack of a clear consensus on their species-level taxonomy. Furthermore, there are currently no reliable DNA sequencing methods to allow for differentiation of the toxigenic potential of these fungi. To address these issues, we performed metabolomic profiling using liquid chromatography high resolution mass spectrometry (LC-HRMS) on 131 Canadian strains of Alternaria to determine their chemotaxonomy. The Alternaria strains were analyzed using principal component analysis (PCA) and unbiased k-means clustering to identify metabolites with significant differences (P < 0.001) between groups. Four populations or ‘chemotypes’ were identified within the strains studied and several known secondary metabolites of Alternaria were identified as distinguishing metabolites.","INSTITUTE":"Agriculture and Agri-Food Canada","DEPARTMENT":"London Research and Development Centre","LABORATORY":"Natural Products Chemistry","LAST_NAME":"Kelman","FIRST_NAME":"Megan","ADDRESS":"1391 Sandford Street, London, Ontario N5V 4T3, Canada","EMAIL":"megan.kelman@canada.ca","PHONE":"519-953-6722","FUNDING_SOURCE":"Agriculture and Agri-Food Canada","CONTRIBUTORS":"Megan J. Kelman, Justin B. Renaud, Keith A. Seifert, Jonathan Mack, Ken K.-C. Yeung and Mark W. Sumarah"},

"STUDY":{"STUDY_TITLE":"Metabolomic profiling of Canadian species of Alternaria","STUDY_SUMMARY":"This study aims to determine the predominant Alternaria species present in Canadian crops, their subsequent substrate distribution and which secondary metabolites are produced. 131 isolates obtained from the Canadian Collection of Fungal Cultures (CCFC) were grown as three-point inoculations on potato dextrose agar (PDA) and grown in the dark for seven days at 25°C. Each strain was extracted with ethyl acetate containing 1% formic acid, and analyzed by high resolution mass spectrometry (HRMS) in full MS mode in both positive and negative ionization modes at 140K resolution. Data were analyzed using principal component analysis (PCA), and groups were assigned based on k-means clustering analysis. All metabolites detected in the peak lists were investigated for significance (P<0.001) between groups using the Kruskal-Wallace test using Benjamini Hochberg false discovery rate (FDR) correction.","INSTITUTE":"Agriculture and Agri-Food Canada","DEPARTMENT":"London Research and Development Centre","LABORATORY":"Natural Products Chemistry","LAST_NAME":"Kelman","FIRST_NAME":"Megan","ADDRESS":"1391 Sandford Street, London, Ontario N5V 4T3, Canada","EMAIL":"megan.kelman@canada.ca","PHONE":"519-953-6722","NUM_GROUPS":"4","TOTAL_SUBJECTS":"128"},

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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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},
{
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{
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{
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},
{
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"Factors":{"Group":"1","Host Plant":"Avena sativa (Canada Western)"},
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},
{
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},
{
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},
{
"Subject ID":"-",
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},
{
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"KAS5515.fullMS.neg.raw"}
},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"KAS5517-blank.raw"}
},
{
"Subject ID":"-",
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"Factors":{"Group":"4","Host Plant":"Secale cereale (Canada Eastern)"},
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},
{
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},
{
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},
{
"Subject ID":"-",
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"Factors":{"Group":"4","Host Plant":"Secale cereale (Canada Eastern)"},
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"KAS5519.fullMS.pos.raw"}
},
{
"Subject ID":"-",
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"Additional sample data":{"RAW_FILE_NAME":"KAS5520.fullMS.neg.raw"}
},
{
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"KAS5520-blank.raw"}
},
{
"Subject ID":"-",
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"Factors":{"Group":"1","Host Plant":"Perennial"},
"Additional sample data":{"RAW_FILE_NAME":"KAS5521.fullMS.neg.raw"}
},
{
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"KAS5521-blank.raw"}
},
{
"Subject ID":"-",
"Sample ID":"MBBC37c.fullMS.neg",
"Factors":{"Group":"2","Host Plant":"Vaccinium angustifolium"},
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},
{
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},
{
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"Factors":{"Group":"-","Host Plant":"-"},
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},
{
"Subject ID":"-",
"Sample ID":"NS1.fullMS.neg",
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"Additional sample data":{"RAW_FILE_NAME":"NS1.fullMS.neg.raw"}
},
{
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"Additional sample data":{"RAW_FILE_NAME":"NS1.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"NS1Foch2-blank",
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"Additional sample data":{"RAW_FILE_NAME":"NS1Foch2-blank.raw"}
},
{
"Subject ID":"-",
"Sample ID":"NSFoch2.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Vitis vinifera"},
"Additional sample data":{"RAW_FILE_NAME":"NSFoch2.fullMS.neg.raw"}
},
{
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"Factors":{"Group":"1","Host Plant":"Vitis vinifera"},
"Additional sample data":{"RAW_FILE_NAME":"NSFoch2.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"RJS1.2a.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Rubus sp."},
"Additional sample data":{"RAW_FILE_NAME":"RJS1.2a.fullMS.neg.raw"}
},
{
"Subject ID":"-",
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"Factors":{"Group":"1","Host Plant":"Rubus sp."},
"Additional sample data":{"RAW_FILE_NAME":"RJS1.2a.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"RJS14a.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Rubus sp."},
"Additional sample data":{"RAW_FILE_NAME":"RJS14a.fullMS.neg.raw"}
},
{
"Subject ID":"-",
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"Factors":{"Group":"1","Host Plant":"Rubus sp."},
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},
{
"Subject ID":"-",
"Sample ID":"RJS14a-blank",
"Factors":{"Group":"-","Host Plant":"-"},
"Additional sample data":{"RAW_FILE_NAME":"RJS14a-blank.raw"}
},
{
"Subject ID":"-",
"Sample ID":"RJS1c.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Rubus sp."},
"Additional sample data":{"RAW_FILE_NAME":"RJS1c.fullMS.neg.raw"}
},
{
"Subject ID":"-",
"Sample ID":"RJS1c.fullMS.pos",
"Factors":{"Group":"1","Host Plant":"Rubus sp."},
"Additional sample data":{"RAW_FILE_NAME":"RJS1c.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"RJS1c-blank",
"Factors":{"Group":"-","Host Plant":"-"},
"Additional sample data":{"RAW_FILE_NAME":"RJS1c-blank.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOM2.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOM2.fullMS.neg.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOM2.fullMS.pos",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOM2.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOM2-blank",
"Factors":{"Group":"-","Host Plant":"-"},
"Additional sample data":{"RAW_FILE_NAME":"TOM2-blank.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3a.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3a.fullMS.neg.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3a.fullMS.pos",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3a.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3b.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3b.fullMS.neg.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3b.fullMS.pos",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3b.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3b-blank",
"Factors":{"Group":"-","Host Plant":"-"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3b-blank.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3c.fullMS.neg",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3c.fullMS.neg.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3c.fullMS.pos",
"Factors":{"Group":"1","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3c.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3d.fullMS.neg",
"Factors":{"Group":"4","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3d.fullMS.neg.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3d.fullMS.pos",
"Factors":{"Group":"4","Host Plant":"Solanum lycopersicum"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3d.fullMS.pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"TOMSTEM3d-blank",
"Factors":{"Group":"-","Host Plant":"-"},
"Additional sample data":{"RAW_FILE_NAME":"TOMSTEM3d-blank.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The majority of fungal isolates were obtained through the Canadian Collection of Fungal Cultures (CCFC) at the Agriculture and Agri-Food Canada in Ottawa, Ontario Canada. Strains from tomato in London, Ontario were isolated by putting tomato stems and fruit in moist chambers, and aseptically transferring Alternaria hypahe and spores after genus level verification under a dissecting microscope. Nova Scotia and Vineland grape and blueberry material were collected similarly.","SAMPLE_TYPE":"Plant","COLLECTION_LOCATION":"London, Ontario; Ottawa, Ontario; Mt. Thom, Nova Scotia; Vineland, Ontario; P.E.I.; Quebec; Dunmore, Alberta; Edmonton, Alberta; Killam, Alberta; Beechy, Saskatchewan; Corrine, Saskatchewan;","STORAGE_CONDITIONS":"-20℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"All fungal strains were grown as three point inoculations on potato dextrose agar (PDA) in the dark at 25°C for seven days, or until colonies reached approximately 4 cm in diameter."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cultures were extracted by removing six agar plugs from both the centre and edges of the three point inoculations using a 6 mm cork borer. Agar plugs were extracted with ethyl acetate containing 1% formic acid. Extracts were dried under nitrogen, and reconstituted with acetonitrile before filtration by 0.45µm PTFE syringe filters."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"LC-MS conditions for negative and positive ionization modes","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Agilent Zorbax Eclipse Plus RRHD C18 (2.1 x 50 mm, 1.8µm)","FLOW_GRADIENT":"0%B held for 0.5 minutes, increased to 100%B over 3.5 minutes. Hold B at 100% for 1.5 minutes, and then return to 0%B over 0.5 minutes","FLOW_RATE":"0.3 mL/min","COLUMN_TEMPERATURE":"35","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"0.1% formic acid in acetonitrile","SAMPLE_INJECTION":"2 µL","CAPILLARY_VOLTAGE":"(-) 3.7 kV; (+) 3.9 kV"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ACQUISITION_DATE":"2015","DATA_FORMAT":".raw"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Data were acquired in full MS-SIM mode at 140,000 resolution over a m/z range of 100-1200","CAPILLARY_TEMPERATURE":"400°C","CAPILLARY_VOLTAGE":"3.9 kV","AUTOMATIC_GAIN_CONTROL":"1e6","MS_RESULTS_FILE":"ST001370_AN002286_Results.txt UNITS:Integrated peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}