Source-Dependent Proteomic and Fatty-Acid Responses of Yak, Holstein Cow, Donkey and Bactrian Camel Colostrum to Short-Time Heat Treatment

Colostrum undergoes rapid compositional changes during the early postpartum period, and standardized sampling is essential for cross-species comparison. In this study, day-3 postpartum milk from yak, Holstein cow, donkey, and Bactrian camel (n = 3 per source), representing an early transitional stage between colostrum and mature milk was analyzed using DIA proteomics and targeted GC-MS fatty-acid profiling. Samples were divided into paired unheated and heat-treated aliquots (72 °C for 15 s). Clear source-dependent differences were observed in both the proteomic and FAME-derived fatty-acid profiles, and these differences remained largely preserved after heating. Heat treatment affected the proteome more extensively than the fatty-acid profile, with 387, 146, 303, and 276 differential proteins identified in yak, Holstein cow, donkey, and Bactrian camel milk, respectively, compared with 14, 6, 0, and 0 differential FAME features. Source × heat-treatment analysis further identified 48 protein features and eight FAME features whose responses differed among the four milk sources. Six protein symbols were shared across all four heat-responsive protein sets, whereas the FAME response was mainly concentrated in yak and Holstein cow milk. Cross-omic integration showed strong agreement between proteomic and fatty-acid profiles at the animal-source level (Procrustes M2 = 0.276, p < 0.001; Mantel r = 0.943, p = 0.001), whereas heat-induced changes were more omics-specific. Overall, animal source was the primary factor associated with the molecular composition of early postpartum milk, whereas short-time heating introduced smaller but clearly source-dependent alterations, particularly at the proteomic level. These source-associated molecular characteristics provide insights into the functional diversity of early lactation milk and support the identification of bioactive components and the development of value-added dairy products.