Capillary electrophoresis combined with 252Cf plasma desorption and electrospray mass spectrometry for the structural characterization of hydrophobic polypeptides using organic solvents.

Capillary electrophoresis (CE) conditions have been developed for the separation of hydrophobic polypeptides, such as fatty acid-acylated peptides, and their subsequent structural identification by 252Cf plasma desorption (PDMS) and electrospray mass spectrometry (ESMS). Salt- and detergent-free aqueous acetic acid buffers containing up to 20% 2-propanol or 25% acetonitrile were employed for CE separations of hydrophobic peptides with (i) untreated, and (ii) 3-aminopropyltrimethoxysilane-derived fused silica capillaries. For both capillary types, electroosmotic flow rates suitable for sample isolation and transfer were determined, and CE separations of polypeptide mixtures were compared for aqueous buffers containing 2-propanol or acetonitrile. For the mass spectrometric identification of CE-separated peptides, a sheath flow sample isolation method was developed for subsequent transfer to PDMS. This procedure enabled the efficient isolation of peptide fractions for PDMS analysis, or alternative microanalytical techniques.