Trypanosoma cruzi produces a long-lasting and diverse antibody response in infected hosts. Recently, with the advent of high-density peptide microarrays, millions of peptides from the complete proteomes of two T. cruzi strains were subjected to extensive immune profiling revealing thousands of discrete antibody-binding peaks and antigenic regions in proteins, from infected human hosts across diverse human populations. Furthermore, hundreds of the identified epitopes were subjected to redundant site-specific mutagenesis to reveal residues important for antibody-binding in these epitopes. This chapter provides software and tools to analyze peptide microarray data in this context and also guiding examples to allow users to re-analyze data in their own ways.