Landscape and m⁶A post-transcriptional regulation of soybean proteome

The soybean is a critical source of vegetable protein, but its proteome remains undercharacterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity with significant differences in protein-transcript abundance across organs. We also map N⁶-methyladenosine (m⁶A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of the proteome and m⁶A methylome identifies a novel regulator in m⁶A methylation. This comprehensive proteomic and m⁶A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.