Text S1 Detailed methods for enzyme activity assays, immunoblots, real-time PCR assays, and measurements of Ang II and Ang-(1-7). (DOC) PepMapper: A Collaborative Web Tool for Mapping Epitopes from Affinity-Selected Peptides Epitope mapping from affinity-selected peptides has become popular in epitope prediction, and correspondingly many Web-based tools have been developed in recent years. However, the performance of these tools varies in different circumstances. To address this problem, we employed an ensemble approach to incorporate two popular Web tools, MimoPro and Pep-3D-Search, together for taking advantages offered by both methods so as to give users more options for their specific purposes of epitope-peptide mapping. The combined operation of Union finds as many associated peptides as possible from both methods, which increases sensitivity in finding potential epitopic regions on a given antigen surface. The combined operation of Intersection achieves to some extent the mutual verification by the two methods and hence increases the likelihood of locating the genuine epitopic region on a given antigen in relation to the interacting peptides. The Consistency between Intersection and Union is an indirect sufficient condition to assess the likelihood of successful peptide-epitope mapping. On average from 27 tests, the combined operations of PepMapper outperformed either MimoPro or Pep-3D-Search alone. Therefore, PepMapper is another multipurpose mapping tool for epitope prediction from affinity-selected peptides. The Web server can be freely accessed at: http://informatics.nenu.edu.cn/PepMapper/ Epitope mapping from affinity-selected peptides has been proven to be a useful approach in identifying native epitopes for immunological applications in recent years [1, 2, 3, 4, 5, 6, 7, 8] . Affinity-selected peptides which are derived from phage-display experiments, also known as mimotopes, are assumed to have similar components with the native epitope [9] . Various ways have been proposed to map the mimotopes back to the genuine epitope. These methods were reviewed and compared in some recent literature [10, 11] . In general, they can be categorized as sequence based [12] , motif based [7, 13] , physicochemical properties based [14] , and graph search based [4, 15, 16] methods. Graph search methods are among the most efficient ways in epitope mapping demonstrated in many recent publications [4, 15, 16] because they take advantages of more information provided by using both the 3D structure of a protein than using the traditional amino acid sequence and the information from mimotope set.