A method for preparing peptide fragments by cleaving a protein using a protease. The method according to the present invention comprises a step for contacting, in a liquid, a porous body (20), in which the substrate protein (25) to be cleaved is immobilized in pores (29), with microparticles (10) which carry the protease (15) immobilized on the surface thereof. In the present invention, the average particle diameter of the microparticles (10) is larger than the average pore diameter of the porous body (20). According to the method of the present invention, the substrate protein (25) that is an antibody can be site-specifically cleaved. By analyzing the peptide fragments that are obtained by the above method by mass spectrometry, etc., the antibody protein can be detected or quantitatively analyzed.