Data-independent acquisition-based quantitative proteomics in plants

Data-independent acquisition (DIA)-based proteomics is increasingly becoming a standard procedure for comprehensive protein analysis in plant systems. This high-throughput approach is now extensively employed to characterize protein dynamics across various plant physiological processes including growth, development, and stress responses. Particularly in plant science, this approach facilitates the discovery of novel disease resistance proteins and regulatory pathways involved in plant defense mechanisms. Continuing advancements in DIA proteomics methodologies bolster its sensitivity, reproducibility, and throughput, thus broadening its utility in botanical research. This review offers a comprehensive overview of the myriad applications of DIA proteomics in elucidating biological processes and molecular mechanisms with a primary focus on plants. Ultimately, it underscores the pivotal role of DIA proteomics in advancing our understanding of plant biological systems, while also discussing future directions and challenges in the field.