Proteomics-based multi-omics reveals m6A-mediated regulation of the plant proteome

Proteins are central to virtually all life processes, making protein-level research essential for gaining deeper insights into plant biology. Recent innovations in mass spectrometry (MS)-based proteomics have enabled precise and high-throughput analyses of plant protein expression, modifications, and interactions (Sang et al., 2025). These advances are transforming our ability to delineate complex regulatory networks and are increasingly being integrated into multi-omics strategies for gene discovery and trait analysis. Notably, two recent studies have delivered the most comprehensive pan-tissue proteomics-centered multi-omics atlases to date in rice and soybean (two of the world's most important crops), uncovering the key role of N⁶-methyladenosine (m⁶A) in post-transcriptional regulation of the plant proteome (Li et al., 2024; Yang et al., 2025).