Summary of Study ST001370

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000936. The data can be accessed directly via it's Project DOI: 10.21228/M8Q114 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001370
Study TitleMetabolomic profiling of Canadian species of Alternaria
Study SummaryThis 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
DepartmentLondon Research and Development Centre
LaboratoryNatural Products Chemistry
Last NameKelman
First NameMegan
Address1391 Sandford Street, London, Ontario N5V 4T3, Canada
Emailmegan.kelman@canada.ca
Phone519-953-6722
Submit Date2020-04-27
Num Groups4
Total Subjects128
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-06-01
Release Version1
Megan Kelman Megan Kelman
https://dx.doi.org/10.21228/M8Q114
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000936
Project DOI:doi: 10.21228/M8Q114
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

Subject:

Subject ID:SU001444
Subject Type:Fungi
Subject Species:Alternaria sp.
Taxonomy ID:1715220

Factors:

Subject type: Fungi; Subject species: Alternaria sp. (Factor headings shown in green)

mb_sample_id local_sample_id Group Host Plant
SA099547KAS5513.fullMS.pos1 Avena sativa (Canada Western)
SA099548KAS5453.fullMS.pos1 Avena sativa (Canada Western)
SA099549KAS5513.fullMS.neg1 Avena sativa (Canada Western)
SA099550KAS5453.fullMS.neg1 Avena sativa (Canada Western)
SA099551KAS5499.fullMS.neg1 Brassica napus (Canada Western Canola)
SA099552KAS5499.fullMS.pos1 Brassica napus (Canada Western Canola)
SA099553KAS5368.fullMS.pos1 Daucus carota
SA099554KAS5368.fullMS.neg1 Daucus carota
SA099555KAS5492.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099556KAS5493.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099557KAS5458.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099558KAS5459.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099559KAS5460.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099560KAS5459.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099561KAS5493.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099562KAS5460.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099563KAS5492.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099564KAS5462.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099565KAS5457.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099566KAS5457.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099567KAS5494.fullMS.pos1 Hordeum vulgare L. (Canada Western)
SA099568KAS5462.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099569KAS5458.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099570KAS5494.fullMS.neg1 Hordeum vulgare L. (Canada Western)
SA099571KAS5321.fullMS.pos1 Lycopersicon esculentum
SA099572KAS5321.fullMS.neg1 Lycopersicon esculentum
SA099573KAS5313.fullMS.neg1 Lycopersicon esculentum
SA099574KAS5313.fullMS.pos1 Lycopersicon esculentum
SA099575KAS5401.fullMS.pos1 Malus domestica
SA099576KAS5401.fullMS.neg1 Malus domestica
SA099577KAS5398.fullMS.pos1 Malus domestica
SA099578KAS5398.fullMS.neg1 Malus domestica
SA099579KAS5521.fullMS.neg1 Perennial
SA099580KAS5274.fullMS.pos1 Perennial
SA099581KAS5521.fullMS.pos1 Perennial
SA099582KAS5319.fullMS.pos1 Perennial
SA099583KAS5319.fullMS.neg1 Perennial
SA099584KAS5309.fullMS.pos1 Perennial
SA099585KAS5295.fullMS.pos1 Perennial
SA099586KAS5309.fullMS.neg1 Perennial
SA099587KAS5274.fullMS.neg1 Perennial
SA099588KAS5324.fullMS.neg1 Perennial
SA099589KAS5377.fullMS.pos1 Perennial
SA099590KAS5377.fullMS.neg1 Perennial
SA099591KAS5301.fullMS.pos1 Perennial
SA099592KAS5378.fullMS.neg1 Perennial
SA099593KAS5293.fullMS.neg1 Perennial
SA099594KAS5378.fullMS.pos1 Perennial
SA099595KAS5293.fullMS.pos1 Perennial
SA099596KAS5301.fullMS.neg1 Perennial
SA099597KAS5295.fullMS.neg1 Perennial
SA099598KAS5365.fullMS.neg1 Perennial
SA099599KAS5300.fullMS.neg1 Perennial
SA099600KAS5373.fullMS.neg1 Perennial
SA099601KAS5300.fullMS.pos1 Perennial
SA099602KAS5373.fullMS.pos1 Perennial
SA099603KAS5322.fullMS.neg1 Perennial
SA099604KAS5380.fullMS.neg1 Perennial
SA099605KAS5324.fullMS.pos1 Perennial
SA099606KAS5380.fullMS.pos1 Perennial
SA099607KAS5305.fullMS.neg1 Perennial
SA099608KAS5305.fullMS.pos1 Perennial
SA099609KAS5307.fullMS.neg1 Perennial
SA099610KAS5325.fullMS.neg1 Perennial
SA099611KAS5382.fullMS.pos1 Perennial
SA099612KAS5325.fullMS.pos1 Perennial
SA099613KAS5382.fullMS.neg1 Perennial
SA099614KAS5365.fullMS.pos1 Perennial
SA099615KAS5322.fullMS.pos1 Perennial
SA099616KAS5307.fullMS.pos1 Perennial
SA099617RJS1.2a.fullMS.neg1 Rubus sp.
SA099618RJS14a.fullMS.pos1 Rubus sp.
SA099619RJS14a.fullMS.neg1 Rubus sp.
SA099620RJS1.2a.fullMS.pos1 Rubus sp.
SA099621RJS1c.fullMS.neg1 Rubus sp.
SA099622RJS1c.fullMS.pos1 Rubus sp.
SA099623KAS5516.fullMS.neg1 Secale cereale (Canada Eastern)
SA099624KAS5516.fullMS.pos1 Secale cereale (Canada Eastern)
SA099625KAS5517.fullMS.pos1 Secale cereale (Canada Eastern)
SA099626KAS5517.fullMS.neg1 Secale cereale (Canada Eastern)
SA099627TOMSTEM3c.fullMS.neg1 Solanum lycopersicum
SA099628TOMSTEM3b.fullMS.pos1 Solanum lycopersicum
SA099629TOM2.fullMS.neg1 Solanum lycopersicum
SA099630TOM2.fullMS.pos1 Solanum lycopersicum
SA099631TOMSTEM3b.fullMS.neg1 Solanum lycopersicum
SA099632TOMSTEM3a.fullMS.pos1 Solanum lycopersicum
SA099633TOMSTEM3c.fullMS.pos1 Solanum lycopersicum
SA099634TOMSTEM3a.fullMS.neg1 Solanum lycopersicum
SA099635KAS5511.fullMS.neg1 Triticum spp. (Amber Durum)
SA099636KAS5510.fullMS.neg1 Triticum spp. (Amber Durum)
SA099637KAS5510.fullMS.pos1 Triticum spp. (Amber Durum)
SA099638KAS5511.fullMS.pos1 Triticum spp. (Amber Durum)
SA099639KAS5485.fullMS.neg1 Triticum spp. (Canada Western Amber Durum)
SA099640KAS5485.fullMS.pos1 Triticum spp. (Canada Western Amber Durum)
SA099641KAS5484.fullMS.pos1 Triticum spp. (Canada Western Amber Durum)
SA099642KAS5484.fullMS.neg1 Triticum spp. (Canada Western Amber Durum)
SA099643KAS5464.fullMS.neg1 Triticum spp. (Canada Western Prairie Spring Red)
SA099644KAS5464.fullMS.pos1 Triticum spp. (Canada Western Prairie Spring Red)
SA099645KAS5465.fullMS.pos1 Triticum spp. (Canada Western Prairie Spring Red)
SA099646KAS5465.fullMS.neg1 Triticum spp. (Canada Western Prairie Spring Red)
Showing page 1 of 4     Results:    1  2  3  4  Next     Showing results 1 to 100 of 338

Collection:

Collection ID:CO001439
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 ID:TR001459
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.

Sample Preparation:

Sampleprep ID:SP001452
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.

Combined analysis:

Analysis ID AN002286 AN002287
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity
Column Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm) Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Integrated peak area Integrated peak area

Chromatography:

Chromatography ID:CH001680
Chromatography Summary:LC-MS conditions for negative and positive ionization modes
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent ZORBAX RRHD Eclipse Plus C18 (50 x 2.1 mm,1.8 µm)
Column Temperature:35
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
Sample Injection:2 µL
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Capillary Voltage:(-) 3.7 kV; (+) 3.9 kV
Chromatography Type:Reversed phase

MS:

MS ID:MS002130
Analysis ID:AN002286
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired in full MS-SIM mode at 140,000 resolution over a m/z range of 100-1200
Ion Mode:POSITIVE
Capillary Temperature:400°C
Capillary Voltage:3.9 kV
Automatic Gain Control:1e6
  
MS ID:MS002131
Analysis ID:AN002287
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired in full MS-SIM mode at 140,000 resolution over a m/z range of 100-1200
Ion Mode:NEGATIVE
Capillary Temperature:400°C
Capillary Voltage:3.7 kV
Automatic Gain Control:1e6
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