Enhanced Analysis of Low-Abundance Proteins in Soybean Seeds Using Advanced Mass Spectrometry.

ABSTRACT: This 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 Hig

SUBMITTER: Meng B 

PROVIDER: S-EPMC11817203 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature