The complexity of an organism's proteome is in part due to the diversity of post-translational modifications present that can direct the location and function of a protein. To address the growing interest in characterizing these modifications, mass spectrometric-based proteomics has emerged as one of the most essential experimental platforms for their discovery. In searching for post-translational modifications within a target set of proteins to global surveys of particularly modified proteins within a given proteome, various experimental MS (mass spectrometry) and allied techniques have been developed. Out of 20 naturally encoded amino acids, lysine is essentially the most highly post-translationally modified residue. This chapter provides a succinct overview of such methods for the characterization of protein lysine modifications as broadly classified, such as methylation and ubiquitination.