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Comparative Proteomic Atlas of Two Soybean Varieties with Contrasting Seed Oil and Protein Content.

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Guangdong Subcenter of the National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

As complex quantitative traits, soybean seed oil and protein contents are governed by dynamic proteome networks that remain largely unknown. Here, we investigated the dynamic changes of the proteome during seed maturation across two soybean varieties with contrasting seed oil and protein content. Through optimizing the detectability of low-abundance proteins and utilizing library-free data-independent acquisition (directDIA) mass spectrometry, we unprecedentedly identified 7414 proteins and 3975 protein groups (PGs), substantially expanding the soybean seed proteome.

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