Characterization of peptides by capillary zone electrophoresis and electrospray ionization quadrupole time-of-flight tandem mass spectrometry

High performance capillary electrophoresis (HPCE) in an off-line combination with electrospray ionization quadrupole time-of-flight (ESI-QTOF) mass spectrometry (MS) has been developed for separation, identification, and compositional analysis of peptides. Two mixtures of peptides from an extracellular matrix have been separated and profiled by CE with UV detection. Introduction of ammonium formate in aqueous/methanol solution at low pH values provided suitable buffer conditions for a good separation of components and reproducibility of experiments. The analytes were identified by subjecting the CE-collected fractions to (+)nanoESI-QTOF-MS and tandem MS with low energy collision induced dissociation (CID). CE/MS analysis of the mixture generated by peptide hydrolysis has been designed to allow both determination of the peptide amino acid composition and ladder sequencing. The strategy presented here could represent a useful preliminary method to serve as a basis for on-line experiments and for further analysis of proteins and their full structural elucidation.