A new strategy of a liquid chromatography (LC)-enzyme linked immunosorbent assay (ELISA) combined with liquid chromatography-mass spectrometry (LC-MS) was developed to identify the epitopic peptides for the antigen in Streptococcus suis. Metallendopeptidase, a potential antigen for S. suis, was digested by trypsin. The tryptic solution was separated by LC under optimal condition and collected into tubes. After it was dried using a cooling vacuum, the immunogenecity of peptides in each tube was investigated by ELISA against its corresponding antibody. All peptides in each tube with positive signals based on ELISA results were identified by LC-MS. Accordingly, six putative peptides of metallendopeptidase were found and synthesized, all of which possessed high antigenicity recognized by the antibody.