Divergent Immunomodulatory Properties of Milk Proteins from Gannan Yak, Cattle-yak, and Holstein Cattle: Insights from a Comparative Proteomics and Murine Model Study

This supplementary dataset supports a comparative proteomic study investigating the immunomodulatory potential of milk proteins from three bovine groups: Gannan yak (Bos grunniens), Gannan cattle-yak (hybrid), and Holstein cattle (Bos taurus). The research hypothesis posited that their distinct genetic backgrounds would result in significantly different milk protein compositions, particularly in immune-related proteins, which could translate into varied immunoregulatory functions.
The data provided here includes processed results from the proteomic analysis that directly inform the study's immunological focus. Table S1 and S2 list the top 30 high-abundance proteins in cattle-yak and Holstein milk, respectively, serving as a baseline to identify key constitutive immune proteins within each milk type. Table S3 is central to the hypothesis, listing the top 20 proteins significantly down-regulated in cattle-yak milk compared to yak milk; this list is prioritized for subsequent enrichment analysis to identify depleted immune pathways in the hybrid. Figure S1 offers quality control (SDS-PAGE, protein/peptide distributions) validating the proteomic depth for reliable comparison. Figure S2, a clustering heatmap of the CYMP vs. YMP comparison, visually confirms the distinct proteomic profiles that underpin the differential immune protein abundance.
The data demonstrates distinct immune-related protein signatures among the three milk types, but similar signature between YMP and CYMP. The identified differentially abundant proteins, form the molecular basis for the study's subsequent in vivo animal experiments designed to compare the immune regulatory capabilities of the three milk protein isolates. It enables reuse for meta-analyses on milk proteins, candidate biomarker verification, and as a reference for designing functional studies on bovine milk bioactivity.
Data were generated from milk samples (n=3 per group). Proteins were extracted, digested, and analyzed by LC-MS/MS. The processed data presented here was used for comparative abundance analysis to inform targeted immunological investigation and downstream animal study design.