Abstract
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 N(6)-methyladenosine (m(6)A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of the proteome and m(6)A methylome identifies a novel regulator in m(6)A methylation. This comprehensive proteomic and m(6)A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.