COMPARATIVE PEPTIDE-MAPPING OF A HEPATITIS-C VIRAL RECOMBINANT PROTEIN BY CAPILLARY ELECTROPHORESIS AND MATRIX-ASSISTED LASER-DESORPTION TIME-OF-FLIGHT MASS-SPECTROMETRY

Capillary electrophoresis (CE) and matrix-assisted laser desorption ti me-of-flight mass spectrometry (MALDI-TOF-MS) were investigated as alt ernatives to sodium dodecyl sulfate (SDS)-polyacrylamide gel electroph oresis for peptide mapping with Staphylococcus aureus protease (V8) of a hydrophobic recombinant hepatitis C virus antigen, HC-31, which req uired 0.1% SDS for solubility. Controls (V8 only) or HC-31 digests wer e extracted with chloroform-methanol-water (1:4:3) to remove SDS, whic h 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 p eaks were very reproducible (R.S.D.<0.016). 25 fragments were resolved by MALDI-TOF-MS, including six smaller peptides (M(r)<13 000) resulti ng from V8 autodigestion. MALDI-TOF-MS indicated that partial cleavage s occurred, primarily at sites where there are paired glutamic and/or aspartic acid residues.