Deep and High-Throughput Proteomic Atlas of Chinese Bovine Colostrum Reveals Regional Signatures

Bovine colostrum (BC) is essential for neonatal survival and human health, owing to its rich bioactive content. However, highly abundant proteins constrain the proteome depth of BC. By integrating magnetic nanoparticle enrichment of low-abundance proteins with a DIA-MS workflow, we achieved an unprecedented depth in BC proteome profiling. Across 463 samples from 10 Chinese provinces, our rapid DIA-MS platform identified 4,558 proteins. Importantly, the identified data set represents an MMN-enriched and DIA-quantifiable proteome space rather than an absolute reconstruction of the entire colostrum proteome. A conserved core of 409 proteins (≥90% of samples) was enriched for immune-, defense-, and transport-related functions. Multivariate analysis revealed a distinctive Heilongjiang (HLJ) profile with reduced abundance of proteins annotated to acute-phase or inflammatory processes and increased abundance of proteins associated with cellular maintenance pathways. Machine learning identified a 9-protein HLJ marker panel that distinguished HLJ from other provinces with near-perfect accuracy (Area Under the Curve, AUC ≈0.99). This study provides the first comprehensive characterization of the BC proteome across 10 Chinese provinces and defines an HLJ-specific biomarker signature, offering tools for traceability and quality control of BC products.