<p>Advancements in mass-spectrometry-based proteomics and metabolomics have significantly improved the ability to screen a wide spectrum of molecules in food matrices. This study provides a comprehensive overview of the principles of mass spectrometry-based proteomics and metabolomics in the analysis of milk products. In particular, this overview provides detailed information on the applications of mass spectrometry-based proteomics and metabolomics for analyzing changes in proteins and metabolites during processing, as well as for evaluating the safety and adulteration of milk products. Profiles of proteins and metabolites secreted by microorganisms in milk have been effectively used to assess the microbiological safety of milk. Furthermore, certain molecules have been used as markers for the evaluation of adulteration in milk products. Therefore, integration of mass spectrometry-based proteomics and metabolomics may be a powerful means in determining the quality of dairy products.</p>