Comparative peptide mapping of a hepatitis C viral recombinant protein by capillary electrophoresis and matrix-assisted laser desorption time-of-flight mass spectrometry

Abstract

Capillary electrophoresis (CE) and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) were investigated as alternatives to sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis for peptide mapping with Staphylococcus aureus protease (V8) of a hydrophobic recombinant hepatitis C virus antigen, HC-31, which required 0.1% SDS for solubility. Controls (V8 only) or HC-31 digests were extracted with chloroform-methanol-water (1:4:3) to remove SDS, which interferes with MALDI-TOF, and high salt content, which affects CE. In two different runs by CE, the elution times of each of 11 peptide peaks were very reproducible ( R. S. D.<0.016). 25 fragments were resolved by MALDI-TOF-MS, including six smaller peptides ( M r<13 000) resulting from V8 autodigestion. MALDI-TOF-MS indicated that partial cleavages occurred, primarily at sites where there are paired glutamic and/or aspartic acid residues.