Among all types of biomolecules, proteins make up a large portion of the core function of cellular processes. Studying the proteins in a cell is called proteomics, and all the proteins which make up this system, the proteome. Proteomics relies on robust and sophisticated liquid chromatography mass spectrometry (LC-MS) instrumentation with highly developed protocols to achieve confident results in peptide and protein identifications. For such applications, it is useful for the chromatographic and mass spectrometric properties of peptides to be well characterized and consistent across all forms which a peptide can be found. These forms are either native, where peptides are found as simple strings of amino acids or be altered with what are called post-translational modifications (PTMs), where a functional group has been added to the protein endogenously (in the cell) or by chemical treatment. These modifications can have drastic ramifications on the analytical properties of peptides and can even affect the protein identification output by artificially altering the observed abundance of a protein within a sample if the diminished intensities on LC-MS are not taken into consideration. Moreover, endogenous modifications often represent a feature of a protein which is being used to communicate within a signalling pathway or alter the function of that protein in the cell, thereby making PTMs an important choice for biological investigations. Unfortunately, despite the importance in studying PTMs, their chromatographic characteristics are rarely reported. In this thesis, the chemical characteristics of various PTMs, general and specific, were uncovered and reported, permitting explanations for standard and ‘anomalous’ retention behaviours for peptides carrying PTMs. The general features across all PTMs studied in our lab over the last 10 years were summarized, while more specific behaviours based on peptide primary structure and the position of the modified amino acid were elucidated for peptides carrying deamidations and HexNAc glycosylations. Moreover, one mode which largely showed promise in investigating PTMs, electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), was studied for its retention properties. This led to the development of a retention time prediction algorithm which explained the sequence-specific behaviour of peptides and general features of PTMs in ERLIC.