High-Resolution Profiling of Lactation-Phase-Specific Whey Proteome in Yak Milk: Multidimensionally Functional Insights from Astral-DIA Analysis

Yak milk, a nutritionally dense dairy product indigenous to high-altitude ecosystems, exhibits unique compositional features distinct from those of bovine milk. The developmental trajectory and functional diversification of its whey proteome across key lactation phases (colostrum, transitional milk, and mature milk) remain poorly understood. This study implemented high-resolution Astral data-independent acquisition (DIA) proteomics to systematically map stage-specific whey proteome dynamics. Quantitative analysis identified 1344, 1334, and 1309 unique whey proteins in colostral, transitional, and mature phases, respectively. Multidimensional functional annotation (GO, KEGG, and EggNOG) revealed stage-specific divergence: colostrum proteins were predominantly associated with immune system processes, while transitional and mature milk proteins shifted toward cell transportation, secretion, and vesicle transportation. Temporal expression patterns were deciphered through mFuzz clustering, identifying nine representative whey proteins. This comprehensive investigation elucidates lactation-stage-specific proteomic signatures and their biological implications, advancing insights into yak milk's bioactive properties.