Proteomic Analysis Reveals Altitude-Associated Changes in Immune-Related Bioactive Substances in Yak Colostrum

Yak colostrum is crucial for the adaptation of newborn calves to the harsh environment of the Qinghai–Tibet Plateau. However, the modulation of its bioactive components along altitudinal gradients and the molecular basis remains incompletely understood. This study evaluated the bioactive components including immune factors, immunoglobulins, growth factors, and antioxidant enzyme activities of yak colostrum collected at low (LAT), medium (MAT), and high altitudes (HAT). Furthermore, quantitative proteomic analysis was used to identify differentially expressed proteins and candidate pathways associated with altitude-related variation. The results showed that along the altitudinal gradient, the levels of total solids, fat, antioxidant enzymes (SOD, GSH-Px, and CAT), β-Lg, IL-2, and IL-6 increased significantly (p < 0.05). Conversely, the concentrations of IL-4, immunoglobulins (IgG, IgA, and IgM), and growth factors (IGF-1, and TGF-β) exhibited a significant decline (p < 0.05). Across the three pairwise comparisons, 489, 625, and 246 DEPs were identified, respectively (fold change > 2, FDR < 0.05), corresponding to 1120 unique DEPs after merging the three lists and removing duplicated protein IDs. KEGG enrichment analysis revealed that DEPs between the LAT and MAT groups were predominantly enriched in the complement and coagulation cascades (FDR ≤ 0.05), whereas those between the LAT and HAT groups were significantly enriched in the NF-κB and AMPK signaling pathways (FDR ≤ 0.05). Integrated WGCNA and STEM analyses further identified MAPK signaling and complement and coagulation cascades as candidate pathways associated with the observed phenotypic variation. Collectively, these findings are consistent with a potential energy-allocation trade-off under high-altitude-associated environmental stress, characterized by coordinated changes in energy-rich nutrients, antioxidant capacity, and immune-related components. From a dairy-resource perspective, these findings may support the characterization and differentiated utilization of yak colostrum with distinct bioactive profiles, providing a basis for the high-value utilization of bioactive components and the development of value-added functional dairy products.