Prefractionation and separation by C8 stationary phase: Effective strategies for integral membrane proteins analysis

► Prefractionation of sample digests was successfully achieved during desalting. ► Prefractionation during desalting could efficiently simplify the sample digests. ► C8 column was found superior to C18 column for hydrophobic peptide separation. ► C8 column separation with prefractionation could favour membrane protein analysis.