To assess the reliability of the differentially abundant proteins (DAPs) identified in DIA proteomics data

This study aimed to identify key molecular regulators of IMF deposition through integrated proteomic and metabolomic analyses in three cattle breeds with distinct fattening characteristics: Guyuan, Simmental, and Japanese Wagyu. We conducted comprehensive profiling of longissimus dorsi muscle samples using data-independent acquisition parallel reaction monitoring (DIA-PRM) proteomics and untargeted metabolomics.