The Dry Secretion Metabolome: LC-MS Profiling Distinguishes Subclinical Mastitis from Healthy Udder Quarters Across the Dry Period in Dairy Cows

The dry period is a critical window of susceptibility to intramammary infection in dairy cows, yet the metabolic environment of the mammary gland during this phase remains largely uncharacterized. The objective of this study was to profile the metabolome of bovine dry secretion fluid from quarters with subclinical mastitis (SCM; SCC ≥ 200,000 cells/mL) and healthy quarters (H; SCC < 200,000 cells/mL) on day 2 (D2) and day 21 (D21) of the dry period (n = 10 per group quarters per group, drawn from a cohort of 41 enrolled Holstein dairy cows) using high-performance chemical isotope labeling liquid chromatography–mass spectrometry (CIL-LC–MS). A total of 474 metabolites were positively identified. At D2, 186 metabolites differed significantly between SCM and H quarters, with dipeptides dominating the upregulated metabolites, indicating active proteolysis in infected quarters. Norepinephrine was the most significantly depleted metabolite (FC = 0.27, p = 3.37 × 10−7), pointing to local catecholamine exhaustion. By D21, only 36 metabolites remained altered, representing an 80.6% attenuation of the SCM signature. Interestingly, temporal changes from D2 to D21 far exceeded disease-related differences, with 316 metabolites shifting in both SCM and healthy quarters, establishing mammary involution as the dominant metabolic event during the dry period. Principal component and PLS-DA analyses confirmed that time, not disease status, was the primary driver of metabolic variation. Pathway analysis revealed significant perturbations in amino acid metabolism, glyoxylate and dicarboxylate metabolism, and tryptophan metabolism. These findings provide the first comprehensive metabolomic map of bovine dry secretion, reveal that subclinical mastitis superimposes a proteolytic and neuroimmune disruption onto the involution process, and identify candidate biomarkers for early detection of intramammary infection during the dry period.