Proteomic Analysis of Antinutritional Protein in Wild and Cultivated Soybean Seeds Based on Four-Dimensional Data-Independent Acquisition and Matrix-Assisted Laser Desorption/Ionization–Mass Spectrometry Imaging

Antinutritional proteins are the primary factors limiting the development of commercial varieties of cultivated soybeans from wild soybean. Four-dimensional data-independent acquisition and matrix-assisted laser desorption/ionization-mass spectrometry imaging were used for proteomic analysis of wild and cultivated soybean seeds. Fifteen antigenic proteins, 8 agglutinins, and 33 protease inhibitors were detected in the seeds. The antigenic proteins, such as Gly m 5, Gly m 6, and P34, were distributed primarily in the embryo and were more abundant in wild soybeans. No significant differences in the amount of agglutinin were observed between wild and cultivated soybeans. Protease inhibitors were primarily enriched in soybean embryos, and their presence in wild soybeans was higher than that in cultivated soybeans. The wild and cultivated soybean embryos showed slightly different distributions of antigenic proteins and protease inhibitors, which were distributed primarily in the hypocotyls and cotyledons. These results can be used to assess the benefits and risks of high antinutritional protein expression.