Peptides are therefore of considerable biological interest and so are methods aimed at identifying and understanding peptide sequence motifs associated with biological processes in health and disease. Indeed, recent developments in large-scale, high-density peptide microarray technologies allow the parallel detection of thousands of sequences in a single experiment, and have been used in a wide range of applications, including antibody-antigen interactions, peptide-MHC interactions, substrate profiling, identification of modification sites (e.g. phosphorylation sites), and other peptide-ligand interactions [3, 4, 5, 6, 7] . One of the major advances of peptide microarrays is the ease of generating large numbers of potential target structures and systematic variants hereof [8] .