Analysis of fragmentation patterns produced by the immunoproteasome and proteasome models. A) BoxPlot of the fragment size distribution obtained with the immunoproteasome and the proteasome models. Not significant difference was observed, using a Wilcoxon test, between the sizes of the fragments generated by each model B) Overlap between the fragments generated by the immunoproteasome and proteasome models represented as the percentage of common sites (black bar) and the percentage of common fragments (grey bar). Fragments were obtained from 100 proteins randomly selected from the Swissprot database. We used the optimal proteasome and immunoproteasome models, which were built on 12-residue peptide fragments.