Size-exclusion chromatography using reverse-phase columns for protein separation

Reverse-phase (RP) liquid chromatography (RPLC) and size-exclusion chromatography (SEC) are methods commonly used for protein/peptide separation, and they are based on distinct principles. This study develops a method using RP columns for size-based separation of protein mixtures. Results show that high concentrations of acetonitrile with trifluoroacetic acid as an acid modifier successfully suppressed interactions between proteins and the stationary phase and allowed the RP column to act as a SEC column to separate proteins based on their molecular weight. The reduction of protein disulfide bonds resulted in an improved correlation between the retention time and molecular weight in the RP-based SEC, which indicates that conformation-dependent SEC retention is less important for disulfide-reduced proteins using a current mobile phase. Importantly, the employed salt-free mobile phase allowed the RP-based SEC system to be directly coupled with online mass spectrometry (MS) analysis. Furthermore, by reducing the flow rate and increasing the column length, the separation efficiency was further improved and no adverse effects due to the prolonged separation were observed, which indicates the potential of this strategy to serve as a first-dimensional separation method for constructing an online multi-dimensional LC system. The size-based separation phenomenon with RP columns was further evaluated using a complex protein mixture (a cell lysate), and compared to conventional SEC, more proteins of the cell lysate were observed following the SEC separation principle, which implies the better generality of usage of the RP-based SEC method for protein separation. In summary, results show that the RP-based SEC is highly efficient in achieving protein fractionation. In addition, the employed salt-free mobile phase provides excellent compatibility of the RP-based SEC with other separation strategies or online mass spectrometric analysis. We anticipate that laboratories using RP-HPLC for protein separation will easily be able to move to the size-based separation mode using the same RP-HPLC system.