The human proteome was downloaded from the NCBI website (www.ncbi.nlm.nih.gov/Genomes/date: 29 march 2006) and contained 34.460 protein sequences. The removal of proteins containing the words: predicted, hypothetic or isoform in the protein description label lead to a final core human proteome of 14,034 human protein sequences. We predicted A2 self-antigens using NetCTL version 1.2 [25, 26] for all these protein sequences (default epitope selection threshold). Repeats were removed, along with a small set of self-peptides, which contained the unknown amino acid (X). The final set consisted of 230,460 predicted human HLA-A2 restricted self-antigens each of length 9.