While the performance of CZE and RPLC have been compared in numerous contexts, the paired analysis of heart, small intestine, and spleen provides an opportunity to explore how proteoforms behave regarding these two separation techniques. Despite requiring similarly long acquisition times, the window of separation for CZE was smaller than RPLC. The difference in separation principle was evident in the relationship between proteoform retention/migration times and mass (Figure ) as well as time and hydrophobicity (Figure ). While there is a strong correlation between mass and retention time with RPLC, no significant correlation was observed between mass and migration time with CZE (Table ). Both separation methods demonstrate a correlation between hydrophobicity and time, but RPLC has a stronger correlation. While CZE was performed with an acidic background electrolyte (pH 2.4), we observed a positive correlation between proteoform hydrophobicity and mass-to-charge ratio (Figure ), which helps to explain the increase in hydrophobicity with migration time (less number of "ionizable" amino acids available per size).