Tandem MS spectra were analyzed by SIRIUS 4, with default parameters. A mass accuracy of 10 ppm was applied for all possible ionizations, using ZODIAC for molecular formula validation and all fallback adducts and available databases for structure searches. CANOPUS was employed to predict chemical classes from fragmentation patterns and molecular fingerprints. Putative compound identities were reported for molecular features with a CSI:FingerID score ≥95% or for those that matched the MS/MS spectra of authentic standards, otherwise, only the predicted chemical class was reported.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS -"],"chromatography_protocol":["Both targeted (authentic standards) and untargeted (unknown molecular features) analyses were performed using an Agilent G6545A LC/QTOF-MS (Agilent Technologies). First, 1 µL of samples were injected and analytes were chromatographically resolved using a ZORBAX RRHD Eclipse Plus C18 column (2.1 × 50 mm, 1.8 μm) and guard column Agilent ESC18 (2.1 x 50mm, 1.8 μm). The binary solvent system consisted of solvent A (H2O + 0.1 % formic acid (FA)) and solvent B (acetonitrile (ACN) + 0.1 % FA), using a flow rate of 0.4 mL/min. The solvent gradient was developed as follows: 10 % B, 0–0.5 min; 50 % B, 6.0 min; 90 % B, 9.10–12.5 min, 100 % B.
"],"publication":["Discovery of pseudobaptigenin synthase in fungal-infected Trifolium pratense roots."],"submitter_affiliation":["University of Toronto"],"submitter_name":["Lee Marie Raytek"],"organism_part":["Plant roots"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Frozen pre-homogenized root tissues were thawed and extracted in 20 µL/mg fresh weight (FW) of 80% MeOH. Samples were vortexed and sonicated in an ultrasonic bath with ice for 20 min, then microcentrifuged at 11,000 x g for 10 min to remove cell debris. The supernatants were transferred, dried down, and stored at −20 º C. Prior to LC-Q-TOF/MS analysis, dried samples were resuspended in 80 % MeOH with 20 ng/µL fluorescein and filtered through 0.22 µm hydrophobic PTFE syringe filters.
"],"organism":["Trifolium pratense"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14741"],"author":["Stéphane Bayen. McGill University. 21111 Lakeshore Rd, Sainte-Anne-de-Bellevue, Quebec H9X 3V9. stephane.bayen@mcgill.ca.","Lee Marie Raytek. University of Toronto. 1265 Military Trail, Scarborough, ON M1C 1A4. leemarie.raytek@mail.utoronto.ca.","Lan Liu. McGill University. 21111 Lakeshore Rd, Sainte-Anne-de-Bellevue, Quebec H9X 3V9. lan.liu@mcgill.ca.","Mehran Dastmalchi. University of Toronto. 1265 Military Trail, Scarborough, ON M1C 1A4. m.dastmalchi@utoronto.ca."],"data_transformation_protocol":["Peak intensities for all identified molecular features were normalized against the internal standard prior to plotting. Compounds that were matched against authentic standards were quantified using calibration curves, and are reported as ug/mg fresh weight (FW).
"],"study_factor":["Infection"],"submitter_email":["leemarie.raytek@mail.utoronto.ca"],"sample_collection_protocol":["Fungi were cultured on potato dextrose solid agar (PDA) media at 25 º C, with a 16:8 h light:dark cycle and 50 % humidity for two weeks prior to plant inoculation. Trifolium pratense (cv. Start) seeds were bleach-sterilized and germinated in the dark for 10 d, prior to their transfer into sterile semi-solid, 1/2x Murashige and Skoog (MS) media in magenta boxes. Seedlings were grown in a tissue culture chamber (22 º C; 16:8 h light:dark cycle; 50 % humidity) for 3 weeks. A single PDA plug taken from the growing fungal hyphal edges was used to inoculate the media at the base of each stem, while agar plugs of pure PDA were used for mock controls. Root tissues were harvested at 3 and 7 dpi, and homogenized using mortar and pestle with liquid N2, then stored at −80 º C.
"],"omics_type":["Metabolomics"],"study_design":["Agilent Technologies, 6545 LC-QTOF/MS","Agilent HPLC","untargeted analysis","Plant roots","untargeted metabolites","experimental blank","triple quadrupole mass spectrometer","Trifolium pratense","targeted metabolites","electrospray-ionisation quadrupole time-of-flight tandem mass spectrometry"],"curator_keywords":["Agilent Technologies, 6545 LC-QTOF/MS","Agilent HPLC","untargeted analysis","Plant roots","untargeted metabolites","experimental blank","Trifolium pratense","triple quadrupole mass spectrometer","targeted metabolites","electrospray-ionisation quadrupole time-of-flight tandem mass spectrometry"],"mass_spectrometry_protocol":["Samples were initially run in both positive and negative polarity scan modes with the following parameters: capillary voltage 4,000 V, fragmentor voltage 150 V; skimmer 65 V; sheath gas temperature 250 ° C; sheath gas flow 10 L/min; nebulizer 30 psig; scan rate 2 spectras; and a mass range of 100–1,100 m/z. Untargeted MS/MS fragmentation of additional features was performed using collision energies (CE) 10, 20, and 40 eV in positive ion mode.
"],"additional_accession":[]},"is_claimable":false,"name":"Discovery of pseudobaptigenin synthase in fungal-infected Trifolium pratense roots","description":"Isoflavonoids, and their pterocarpan derivatives, are important phytoalexin defense molecules in legumes (Fabaceae). They are commonly associated with antimicrobial activity and thought to be synthesized de novo or accumulated in response to microbial pathogens. Comparative metabolomics of Fusarium oxysporum or Phoma medicaginis-infected red clover roots reveals dynamic regulation of isoflavonoid metabolic flux. Using both a targeted (authentic standards) and untargeted (MS/MS of unknown features) approach, we identified over 40 putative (iso)flavonoid structures, including the highly abundant O-methylated isoflavones (formononetin and biochanin A), many glucosyl- and malonyl-derivatives, and various pterocarpan species.
","dates":{"publication":"2026-06-11","submission":"2026-06-11"},"accession":"MTBLS14741","cross_references":{}}