Pathogen-induced red pigmentation uncovers a conserved floral defense in Asteraceae

This Zenodo record contains processed LC–MS/MS metabolomics data and downstream analysis outputs for Chrysanthemum morifolium white-flower petals (mock vs Botrytis cinerea infected), including feature detection and quantification (MZmine), feature-based molecular networking (GNPS2 FBMN/IIMN), molecular formula and structure prediction (SIRIUS with CANOPUS), and statistical analysis (FBMNStats).

Raw LC–MS/MS and mzXML files are deposited in MassIVE under accession numbers MSV000100849 (white flower cultivars: Bride, 72507, Aristotle) and MSV000100850 (ResQ flower petals). The GNPS2 FBMN task is available at: https://gnps2.org/status?task=37f4e9bbba4e4a65afcdb9496e27d211

Software versions:ProteoWizard (MSConvert) v3.0.24207MZmine v4.4.3GNPS2 (Feature-Based Molecular Networking workflow)SIRIUS v6.1 (project file included)FBMNStats (as described in Pakkir Shah et al., 2025)

Repository contents:

mzmine_output/white_flowers.mzmine – MZmine project file containing full processing parameters.white_flowers.mzmwizard – MZmine wizard/batch configuration file.white_flowers_iimn_gnps_quant.csv – Feature quantification table (peak intensities per sample; each row corresponds to one m/z–retention time feature).white_flowers_iimn_gnps.mgf – MS/MS spectra file exported for GNPS2 FBMN.white_flowers_iimn_gnps_edges_msannotation.csv – Ion identity edge table linking related features (adducts, in-source fragments, multimers).

GNPS2_Network/gnps_fbmn_network – Cytoscape-compatible FBMN network export.metadata_supernatant_and_standards.csv – Metadata file used for GNPS2 analysis (sample grouping and standards).

SIRIUS_output/sirius_annotation_white_flowers_mock_vs_infected.sirius – Complete SIRIUS project file.formula_identifications.tsv – Predicted molecular formulas.structure_identifications.tsv – Predicted structures.denovo_structure_identifications.tsv – De novo structure predictions.canopus_formula_summary.tsv – CANOPUS compound class predictions (formula level).canopus_structure_summary.tsv – CANOPUS compound class predictions (structure level).spectral_matches.tsv – Exact spectral library matches.spectral_matches_analog.tsv – Analog spectral matches.final_annotation_table.csv – Curated annotation table integrating GNPS and SIRIUS outputs.

FBMNstat/fbmnstat_results_white_flowers.xlsx – Statistical analysis results identifying differentially abundant features between mock and infected samples.

FBMN nodes represent LC–MS features (m/z–retention time pairs); therefore, multiple nodes may share the same annotation due to different adduct forms, isotopes, in-source fragments, or chromatographically separated isomers. Complete annotation details for all features are provided in the SIRIUS output tables and are available in the  final_annotation_table.csv file.