DOI: 10.5061/dryad.qnk98sfv2
title: Machine learning–enabled non–targeted metabolomics reveals nutritional and metabolic responses of <em>Brachypodium distachyon</em> to drought and elevated CO<sub>2</sub>

description: Rising atmospheric CO2, coupled with intensified drought in many regions,
 impacts the physiology of C3 plants beyond photosynthesis and carbon
 metabolism. The interaction between CO2 and drought affects many plant
 nutrient concentrations, reducing the CO2 fertilization effect in natural
 systems, increasing agrochemical use, and reducing the nutritive content
 of crops. To address these challenges, we investigated nutrient dynamics
 in Brachypodium distachyon, a model for C3 cereal grasses, under ambient
 (400 ppm) and elevated (800 ppm) CO2, factorially combined with
 well-watered or drought treatments. Integrative analyses of plant
 physiology, ionomics, transcriptomics, and non-targeted metabolomics
 revealed that plant elemental composition and metabolomic responses to
 elevated CO2 strongly depend on water availability. Elevated CO2 and
 drought impaired nitrogen status, with root nitrate uptake being more
 negatively affected than ammonium uptake. However, elevated CO2 increased
 iron partitioning in leaves under drought, potentially driven by enhanced
 carbon availability, facilitating chelator synthesis for iron
 translocation. The high accumulation of sphingolipids in roots under
 combined stresses suggests a protective role against ionome imbalances.
 These findings highlight how environmental stressors shape plant nutrient
 dynamics, providing insights that may improve modeling ecosystem response
 or guide agricultural practices and breeding strategies to optimize
 nutrient management under changing climate conditions. 
description: # Machine learning–enabled non–targeted metabolomics reveals nutritional
 and metabolic responses of *Brachypodium distachyon* to drought and
 elevated CO~2~ This dataset contains raw LC–MS (.mzML) and processed
 metabolite feature tables for shoot and root tissues of *Brachypodium
 distachyon* exposed to factorial combinations of ambient vs elevated CO~2~
 and control vs drought water regimes. Each .mzML corresponds to a single
 biological replicate. Processed tables provide integrated peak areas, peak
 heights, and signal-to-noise ratios. These data were used in multivariate
 and machine learning analyses described in the accompanying manuscript (J
 Exp Bot 2025,
 [https://doi.org/10.1093/jxb/eraf382](https://doi.org/10.1093/jxb/eraf382)). ## **Descriptions** ### **Raw data** * **DesMarais_et_al_JEXBOT2025_PositiveMode_mzML.zip** Centroided LC–MS data acquired in positive ionization mode. Each file corresponds to one biological sample. * **DesMarais_et_al_JEXBOT2025_NegativeMode_mzML.zip** Centroided LC–MS data acquired in negative ionization mode. Each .mzML filename encodes treatment, replicate, and tissue: * **Treatment codes**: * 400CR, 400CS, 400DR, 400DS = 400 ppm CO~2~; Control or Drought; Root or Shoot * 800CR, 800CS, 800DR, 800DS = 800 ppm CO~2~; Control or Drought; Root or Shoot * **Replicate**: biological replicate number (1, 2, 3) * **Tissue**: Root or Shoot ## **Processed feature tables (tab-delimited .txt)** **Positive mode** * **DesMarais_et_al_JEXBOT2025_PositiveMode_area.txt** — Peak areas * **DesMarais_et_al_JEXBOT2025_PositiveMode_height.txt** — Peak heights * **DesMarais_et_al_JEXBOT2025_PositiveMode_sn.txt** — Signal-to-noise ratios **Negative mode** * **DesMarais_et_al_JEXBOT2025_NegativeMode_area.txt** — Peak areas * **DesMarais_et_al_JEXBOT2025_NegativeMode_height.txt** — Peak heights * **DesMarais_et_al_JEXBOT2025_NegativeMode_sn.txt** — Signal-to-noise ratios #### **Table structure** Each processed table (area, height, S/N) includes the following columns: * **Alignment ID** — unique feature identifier assigned by software * **Average Rt (min)** — retention time in minutes * **Average Mz** — average m/z of detected feature * **Metabolite name** — putative annotation if available * **Adduct type** — ion adduct (e.g., [M+H]+, [M-H]−) * **Post curation result** — curation status flag * **Fill %** — feature filling rate across samples * **MS/MS assigned** — whether MS/MS spectrum is assigned * **Reference RT / m/z** — reference values for annotation * **Formula** — chemical formula (if annotated) * **Ontology** — compound class/ontology assignment * **INCHIKEY** — InChIKey identifier * **SMILES** — SMILES string * **Annotation tag (VS1.0)** — annotation confidence tag * **RT matched / m/z matched / MS/MS matched** — matching criteria used * **Comment** — notes on annotation * **Manually modified for quantification / annotation** — user curation flags * **Isotope tracking parent ID/weight number** — isotope-tracking metadata * **Total score** — overall annotation confidence score * **RT similarity / Dot product / Reverse dot product / Fragment presence %** — spectral matching metrics * **S/N average** — signal-to-noise ratio * **Spectrum reference file name** — reference spectrum file * **MS1 isotopic spectrum / MS/MS spectrum** — spectral data references Following these metadata columns, each table contains **sample-level intensity values** as additional columns (sample IDs follow the .mzML naming scheme, e.g., 400CR_1, 800DS_3). ## **Code / Software** * **Raw file conversion**: ProteoWizard *msConvert* (centroided). * **Feature detection and quantification**: MS-DIAL v4.9. * All exported tables were used directly in multivariate and machine learning analyses performed in R (v4.3.1) and Python (v3.10). No scripts are included in this Dryad submission. Processing workflows are described in the manuscript and Supporting Information. ## **File-level descriptions** **DesMarais_et_al_JEXBOT2025_PositiveMode_mzML.zip** — Centroided raw LC–MS files, positive ionization. **DesMarais_et_al_JEXBOT2025_PositiveMode_area.txt** — Feature table with peak area values. **DesMarais_et_al_JEXBOT2025_PositiveMode_height.txt** — Peak heights. **DesMarais_et_al_JEXBOT2025_PositiveMode_sn.txt** — Signal-to-noise ratios. **DesMarais_et_al_JEXBOT2025_NegativeMode_mzML.zip** — Centroided raw LC–MS files, negative ionization. **DesMarais_et_al_JEXBOT2025_NegativeMode_area.txt** — Peak areas (filename typo retained). **DesMarais_et_al_JEXBOT2025_NegativeMode_height.txt** — Peak heights. **DesMarais_et_al_JEXBOT2025_NegativeMode_sn.txt** — Signal-to-noise ratios. ## **Contact** * Hsin-Fang Chang — [hfchang@mit.edu](mailto:hfchang@mit.edu) * David Des Marais — [dldesmar@mit.edu](mailto:dldesmar@mit.edu)