PepMapper, a combination of both MimoPro and a modified version of Pep-3D-Search together, sets a collaborative Web platform, on which users can conveniently conduct peptideepitope mappings. In addition to the normal process of either MimoPro or Pep-3D-Search alone, the combined operation of Union captures the concept of exploring as many associated peptides as possible from both methods and thus increases sensitivity in finding potential epitopic regions on a given antigen surface. The Intersection operation of PepMapper realizes largely the concept of mutual verification by the two methods and hence increases the likelihood of locating the genuine epitopic region on a given antigen with respect to the interacting peptides. The Consistency between Intersection and Union can be used as an indirect sufficient condition to assess the likelihood of successful peptide-epitope mapping.