**5. Conclusions**

Advances in separation and mass spectrometry capabilities, enable our abilities to identify and characterize proteins and their PTMs. This chapter provides an overview of proteomics investigations in goat milk, from identifying major milk proteins to comprehensive analysis in different fractions and PTMs. Many challenges still exist, but technological advances have led to an increased in research contributing to a better understanding of the proteomic analysis of goat milk. Low-abundance proteins and disease-specific proteins have been identified as potential biomarkers. Using proteomics strategies, the efforts of our group and others have shed some light on the role of APPs during coliform mastitis and other diseases in goats. The host response during infection and related changes in the goat milk proteome remains comparatively limited. Nonetheless, our comparative proteomic analysis suggests that the caprine host response to endotoxin could differ from other ruminant species. Finally, our precise characterization of casein phosphorylation in goat milk before and after challenge with LPS offers new insights into protein modulations in goat milk during mastitis.
