Post-translational modifications are highly dynamic and known to regulate many cellular processes. Both the site and the stoichiometry of modification of a given protein sequence can have profound effects on the regulation of protein function. Thus, the identification of sites of post-translational modification is crucial for fully deciphering the biological roles of any given protein. The acute regulation and typically low stoichiometry of many post-translational modifications makes characterization of the sites of modification challenging. Thus, the development of analytical strategies to aid the selective enrichment and characterization of these species is paramount. Ongoing developments in mass spectrometry resulting in increased speed and sensitivity of analysis mean that mass spectrometry has become the ideal analytical tool for the qualitative and quantitative analysis of protein modifications. This chapter provides an overview of the most popular LC-MS/MS-based strategies for the enrichment of modified peptides/proteins and mass spectrometric workflows targeted toward the analysis of specific post-translationally modified analytes.