Analysis of Modified Plant Metabolites Using Widely Targeted Metabolite Modificomics

Metabolite modifications play a critical role in enhancing plants' adaptability to environmental changes and serve as a major source of functional diversity in metabolites. However, current metabolomics approaches are limited to targeted analyses of a small number of known modified metabolites and lack comprehensive, large-scale studies of plant metabolite modifications. Here, we describe a widely targeted metabolite modificomics (WTMM) strategy, developed using ultra-high-performance liquid chromatography-quadrupole linear ion trap (UHPLC-Q-Trap) and ultra-high-performance liquid chromatography-Q-Exactive Orbitrap (UHPLC-QE-Orbitrap) technologies. This strategy enables high-throughput identification and sensitive quantification of modified metabolites. Using tomato as a model, we conducted a metabolite modificomics study and constructed a WTMM database, identifying 165 novel modified metabolites. The WTMM strategy is broadly applicable and can be extended to the study of other plant species. Key features • WTMM enables large-scale detection and quantitative analysis of plant-modified metabolites. • Integration of UHPLC-Q-Trap and UHPLC-QE-Orbitrap technologies. • The WTMM database is extensible and applicable to other plant species.