iProXProteomicsYang ZhaoGlycine Maxhttp://www.iprox.org/page/project.html?id=IPX0008800000zhaoy@nim.ac.cnNational Institute of MetrologyiProXThis study presents an advanced approach for the comprehensive analysis of low-abundance proteins in soybean seeds, addressing challenges posed by high-abundance storage proteins. We compared the effectiveness of Data-Dependent Acquisition (DDA), Data-Independent Acquisition (DIA), and BoxCar mass spectrometry techniques to identify low-abundance proteins in two types of soybean seeds: High-Oil and High-Protein seeds. The results indicate that the DIA method, and particularly the BoxCar methods, significantly improve the detection of low-abundance proteins compared to DDA, offering deeper insights into soybean seed biology. Specifically, BoxCar-based analysis revealed distinct proteomic differences between High-Oil and High-Protein seeds, highlighting more active metabolic processes in High-Oil seeds. Additionally, several key proteins were identified and annotated as uniquely expressed in either High-Oil or High-Protein seeds. These findings emphasize the importance of advanced proteomic techniques, such as BoxCar, in deepening our understanding of soybean seed biology and supporting breeding strategies to improve nutritional qualities.Enhanced Analysis of Low-Abundance Proteins in Soybean Seeds Using Advanced Mass Spectrometry.Meng Bo B, Huang Yuanyuan Y, Lu Ao A, Liao Huanyue H, Zhai Rui R, Gong Xiaoyun X, Dong Lianhua L, Jiang You Y, Dai Xinhua X, Fang Xiang X, Zhao Yang YfalseComparative Analysis of Soybean Seed Proteome Based on Different Mass Spectrometry Acquisition StrategiesThis study established a soybean seed proteome database and analyzed the raw mass spectrometry data of BoxCar and DIA on MaxQuant based on this database. Subsequently, the three mass spectrometry acquisition strategies, DDA, DIA and BoxCar, were compared for their depth of protein identification, data stability, and effectiveness of their use in differential proteomics.Thu May 16 00:00:00 GMT+01:00 2024PXD052278384739940716