Abstract: Matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF-MS), in combination with immunoaffinity provided a powerful tool for determining epitope(antigenic determinant) in protein. The linear epitope of the β₂-microglobulin was characterized in the paper. The method as follows: at first β₂-microglobulin was digested by a proteolytic enzyme to produce an appropriate set of peptide fragments, then peptide fragments containing the linear epitope were selected and separated from the pool of peptide fragments by immunoprecipitation with the monoclonal antibody. The agarose beads were collected carefully after the reaction. Unbound peptides would be washed away, while the peptides containing the epitope would remain bound to the immobilized antibody after the beads were washed several times with appropriate buffer. At last the masses of the bound peptides were identified directly by MALDI-TOF MS. Using Endoproteinase Glu-C Endoproteinase Lys-C and Trypsin in the experiment, the linear epitope of β₂-microglobulin was located within peptide fragment 59—69, that is, DWSFYLLYYTE.

Key words: MALDI-TOF-MS, Immunoaffinity, β₂-Microglobulin, Linear epitope, Monoclonal antibody