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.
| Study ID | ST001370 |
| 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 |
| megan.kelman@canada.ca | |
| Phone | 519-953-6722 |
| Submit Date | 2020-04-27 |
| Num Groups | 4 |
| Total Subjects | 128 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-06-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA099547 | KAS5513.fullMS.pos | 1 | Host Plant:Avena sativa (Canada Western) |
| SA099548 | KAS5453.fullMS.pos | 1 | Host Plant:Avena sativa (Canada Western) |
| SA099549 | KAS5513.fullMS.neg | 1 | Host Plant:Avena sativa (Canada Western) |
| SA099550 | KAS5453.fullMS.neg | 1 | Host Plant:Avena sativa (Canada Western) |
| SA099551 | KAS5499.fullMS.neg | 1 | Host Plant:Brassica napus (Canada Western Canola) |
| SA099552 | KAS5499.fullMS.pos | 1 | Host Plant:Brassica napus (Canada Western Canola) |
| SA099553 | KAS5368.fullMS.pos | 1 | Host Plant:Daucus carota |
| SA099554 | KAS5368.fullMS.neg | 1 | Host Plant:Daucus carota |
| SA099555 | KAS5492.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099556 | KAS5493.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099557 | KAS5458.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099558 | KAS5459.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099559 | KAS5460.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099560 | KAS5459.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099561 | KAS5493.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099562 | KAS5460.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099563 | KAS5492.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099564 | KAS5462.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099565 | KAS5457.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099566 | KAS5457.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099567 | KAS5494.fullMS.pos | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099568 | KAS5462.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099569 | KAS5458.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099570 | KAS5494.fullMS.neg | 1 | Host Plant:Hordeum vulgare L. (Canada Western) |
| SA099571 | KAS5321.fullMS.pos | 1 | Host Plant:Lycopersicon esculentum |
| SA099572 | KAS5321.fullMS.neg | 1 | Host Plant:Lycopersicon esculentum |
| SA099573 | KAS5313.fullMS.neg | 1 | Host Plant:Lycopersicon esculentum |
| SA099574 | KAS5313.fullMS.pos | 1 | Host Plant:Lycopersicon esculentum |
| SA099575 | KAS5401.fullMS.pos | 1 | Host Plant:Malus domestica |
| SA099576 | KAS5401.fullMS.neg | 1 | Host Plant:Malus domestica |
| SA099577 | KAS5398.fullMS.pos | 1 | Host Plant:Malus domestica |
| SA099578 | KAS5398.fullMS.neg | 1 | Host Plant:Malus domestica |
| SA099579 | KAS5521.fullMS.neg | 1 | Host Plant:Perennial |
| SA099580 | KAS5274.fullMS.pos | 1 | Host Plant:Perennial |
| SA099581 | KAS5521.fullMS.pos | 1 | Host Plant:Perennial |
| SA099582 | KAS5319.fullMS.pos | 1 | Host Plant:Perennial |
| SA099583 | KAS5319.fullMS.neg | 1 | Host Plant:Perennial |
| SA099584 | KAS5309.fullMS.pos | 1 | Host Plant:Perennial |
| SA099585 | KAS5295.fullMS.pos | 1 | Host Plant:Perennial |
| SA099586 | KAS5309.fullMS.neg | 1 | Host Plant:Perennial |
| SA099587 | KAS5274.fullMS.neg | 1 | Host Plant:Perennial |
| SA099588 | KAS5324.fullMS.neg | 1 | Host Plant:Perennial |
| SA099589 | KAS5377.fullMS.pos | 1 | Host Plant:Perennial |
| SA099590 | KAS5377.fullMS.neg | 1 | Host Plant:Perennial |
| SA099591 | KAS5301.fullMS.pos | 1 | Host Plant:Perennial |
| SA099592 | KAS5378.fullMS.neg | 1 | Host Plant:Perennial |
| SA099593 | KAS5293.fullMS.neg | 1 | Host Plant:Perennial |
| SA099594 | KAS5378.fullMS.pos | 1 | Host Plant:Perennial |
| SA099595 | KAS5293.fullMS.pos | 1 | Host Plant:Perennial |
| SA099596 | KAS5301.fullMS.neg | 1 | Host Plant:Perennial |
| SA099597 | KAS5295.fullMS.neg | 1 | Host Plant:Perennial |
| SA099598 | KAS5365.fullMS.neg | 1 | Host Plant:Perennial |
| SA099599 | KAS5300.fullMS.neg | 1 | Host Plant:Perennial |
| SA099600 | KAS5373.fullMS.neg | 1 | Host Plant:Perennial |
| SA099601 | KAS5300.fullMS.pos | 1 | Host Plant:Perennial |
| SA099602 | KAS5373.fullMS.pos | 1 | Host Plant:Perennial |
| SA099603 | KAS5322.fullMS.neg | 1 | Host Plant:Perennial |
| SA099604 | KAS5380.fullMS.neg | 1 | Host Plant:Perennial |
| SA099605 | KAS5324.fullMS.pos | 1 | Host Plant:Perennial |
| SA099606 | KAS5380.fullMS.pos | 1 | Host Plant:Perennial |
| SA099607 | KAS5305.fullMS.neg | 1 | Host Plant:Perennial |
| SA099608 | KAS5305.fullMS.pos | 1 | Host Plant:Perennial |
| SA099609 | KAS5307.fullMS.neg | 1 | Host Plant:Perennial |
| SA099610 | KAS5325.fullMS.neg | 1 | Host Plant:Perennial |
| SA099611 | KAS5382.fullMS.pos | 1 | Host Plant:Perennial |
| SA099612 | KAS5325.fullMS.pos | 1 | Host Plant:Perennial |
| SA099613 | KAS5382.fullMS.neg | 1 | Host Plant:Perennial |
| SA099614 | KAS5365.fullMS.pos | 1 | Host Plant:Perennial |
| SA099615 | KAS5322.fullMS.pos | 1 | Host Plant:Perennial |
| SA099616 | KAS5307.fullMS.pos | 1 | Host Plant:Perennial |
| SA099617 | RJS1.2a.fullMS.neg | 1 | Host Plant:Rubus sp. |
| SA099618 | RJS14a.fullMS.pos | 1 | Host Plant:Rubus sp. |
| SA099619 | RJS14a.fullMS.neg | 1 | Host Plant:Rubus sp. |
| SA099620 | RJS1.2a.fullMS.pos | 1 | Host Plant:Rubus sp. |
| SA099621 | RJS1c.fullMS.neg | 1 | Host Plant:Rubus sp. |
| SA099622 | RJS1c.fullMS.pos | 1 | Host Plant:Rubus sp. |
| SA099623 | KAS5516.fullMS.neg | 1 | Host Plant:Secale cereale (Canada Eastern) |
| SA099624 | KAS5516.fullMS.pos | 1 | Host Plant:Secale cereale (Canada Eastern) |
| SA099625 | KAS5517.fullMS.pos | 1 | Host Plant:Secale cereale (Canada Eastern) |
| SA099626 | KAS5517.fullMS.neg | 1 | Host Plant:Secale cereale (Canada Eastern) |
| SA099627 | TOMSTEM3c.fullMS.neg | 1 | Host Plant:Solanum lycopersicum |
| SA099628 | TOMSTEM3b.fullMS.pos | 1 | Host Plant:Solanum lycopersicum |
| SA099629 | TOM2.fullMS.neg | 1 | Host Plant:Solanum lycopersicum |
| SA099630 | TOM2.fullMS.pos | 1 | Host Plant:Solanum lycopersicum |
| SA099631 | TOMSTEM3b.fullMS.neg | 1 | Host Plant:Solanum lycopersicum |
| SA099632 | TOMSTEM3a.fullMS.pos | 1 | Host Plant:Solanum lycopersicum |
| SA099633 | TOMSTEM3c.fullMS.pos | 1 | Host Plant:Solanum lycopersicum |
| SA099634 | TOMSTEM3a.fullMS.neg | 1 | Host Plant:Solanum lycopersicum |
| SA099635 | KAS5511.fullMS.neg | 1 | Host Plant:Triticum spp. (Amber Durum) |
| SA099636 | KAS5510.fullMS.neg | 1 | Host Plant:Triticum spp. (Amber Durum) |
| SA099637 | KAS5510.fullMS.pos | 1 | Host Plant:Triticum spp. (Amber Durum) |
| SA099638 | KAS5511.fullMS.pos | 1 | Host Plant:Triticum spp. (Amber Durum) |
| SA099639 | KAS5485.fullMS.neg | 1 | Host Plant:Triticum spp. (Canada Western Amber Durum) |
| SA099640 | KAS5485.fullMS.pos | 1 | Host Plant:Triticum spp. (Canada Western Amber Durum) |
| SA099641 | KAS5484.fullMS.pos | 1 | Host Plant:Triticum spp. (Canada Western Amber Durum) |
| SA099642 | KAS5484.fullMS.neg | 1 | Host Plant:Triticum spp. (Canada Western Amber Durum) |
| SA099643 | KAS5464.fullMS.neg | 1 | Host Plant:Triticum spp. (Canada Western Prairie Spring Red) |
| SA099644 | KAS5464.fullMS.pos | 1 | Host Plant:Triticum spp. (Canada Western Prairie Spring Red) |
| SA099645 | KAS5465.fullMS.pos | 1 | Host Plant:Triticum spp. (Canada Western Prairie Spring Red) |
| SA099646 | KAS5465.fullMS.neg | 1 | Host Plant:Triticum spp. (Canada Western Prairie Spring Red) |
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 |
