Mass Spectrometry-Based Integrated Multiomics Platforms for Medicinal Plant Analysis

Plant-based multiomics approaches provide powerful tools for elucidating metabolic regulation, biochemical diversity, and functional responses to genetic and environmental variation. However, plant matrices pose unique analytical challenges due to their chemical complexity, high levels of secondary metabolites, and strong matrix effects that can compromise reproducibility if workflows are not carefully standardized. This article presents a comprehensive and integrated set of protocols for untargeted plant metabolomics, lipidomics, and proteomics, coupled with robust data processing, statistical analysis, and multiomics integration strategies. The protocols describe harmonized workflows for sample collection, preparation, and analysis using gas chromatography-mass spectrometry (GC-MS)-based metabolomics, liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-qTOF-MS)-based metabolomics, liquid chromatography-mass spectrometry (LC-MS)-based lipidomics, and microflow LC-MS/MS-based proteomics. Emphasis is placed on critical parameters specific to plant matrices, including complete solvent removal prior to GC-MS derivatization, optimized MS/MS acquisition strategies for high-confidence annotation, and quality control-driven experimental design. Detailed guidance is provided for instrument maintenance, QC strategies, and prevention of analytical artifacts. In addition, the article outlines best practices for data preprocessing, metabolite and lipid annotation, statistical analysis, pathway mapping, and integration of metabolomics with proteomics data to support biologically meaningful interpretation. Collectively, these protocols enable reproducible, high-quality plant multiomics studies and are suitable for both method development and large-scale comparative analyses across plant species, tissues, and experimental conditions. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Plant material collection, handling, and extraction processing Support Protocol 1: Soxhlet extraction Alternate Protocol 1: Dichloromethane (DME)-based sample preparation for lipidomics Alternate Protocol 2: Methyl-tert-butyl ether (MTBE)-based sample preparation for lipidomics Basic Protocol 2: GC-MS-based metabolomics analysis Basic Protocol 3: LC-qTOF-MS-based metabolomics analysis Basic Protocol 4: LC-MS-based lipidomics analysis Basic Protocol 5: Microflow LC-MS/MS-based proteomics analysis Basic Protocol 6: Multiomics data integration and statistical analysis.