Liquid chromatography paired with mass spectrometry (LC-MS) is one of the most commonly used analytical techniques for the study of proteins and their modifications. Many of these modifications play an important role in the structure, function, or interaction of proteins, and need to be separated and identified to understand their impact or abundance. While reversed-phase (RP) chromatography had long been the chromatographic method of choice for proteomics, we show that hydrophilic interaction liquid chromatography (HILIC) is not only capable of separating polar peptides that do not retain on RP columns, but that it can allow for accurate retention time prediction. This work describes the development and validation of a HILIC peptide prediction model that is capable of predicting the retention of native peptides or peptides with common hydrophilic modifications such as glycosylation (N- and O-linked), deamidation of asparagine, isomerization of aspartic acid, and oxidation of methionine. Coefficients describing the extent of hydrophilicity were derived for all of the amino acids and modifications, and it was found that the prediction of peptide retention is incredibly accurate (R2 = 0.946). Predicted retention times can be calculated by summing the coefficients for a peptide sequence, and this has the potential for quicker analyses, as peptides can be identified by their mass-to-charge ratio (m/z) and retention time, and can also increase in the confidence of identifications including isomeric structures as well as allow for less time spent looking for the peptide of interest in targeted approaches. The separation of peptides with these modifications is also detailed, as HILIC is capable of fully separating native peptides from their modified forms to allow for quantitation. While some of the modifications add a substantial mass to the peptide, others, such as deamidation of asparagine or isomerization of aspartic acid, have minimal to zero mass difference and barely change the overall structure of the peptide, which can be difficult to identify simply using MS. Thus, chromatography needs to be utilized to separately identify the similar analytes. In addition to showing complete separation between native and modified peptides, we show that the separation using HILIC is consistent and predictable.