High-throughput comprehensive peptide mapping of proteins by multiplexed capillary electrophoresis

A novel multimodal method for peptide mapping of proteins by multiplexed capillary electrophoresis (CE) is presented. By combining charge to size separations in four different channels and micellar electrokinetic chromatography for hydrophobicity-based separations in two different channels in a 96-capillary array, peptide fragments of digested proteins were readily resolved and showed unique fingerprints. Each capillary spanned several diodes in a photodiode array (PDA) for absorption measurement. The 96 capillaries were monitored simultaneously at 214 nm by a single PDA element with 1024 diodes, and analysis was completed within 45 min. This demonstrates that it is possible to rapidly screen biotechnological products as well as to efficiently optimize separation conditions in CE by a combinatorial approach.