Supplementary Figure 5: Fragmentation efficiency between residue pairs.

Fragmentation efficiencies were calculated for b- and y- fragment ions generated between [X] (y-axis) and [Z] (x-axis) residues in A-A-A-[X]-[Z]-A-A-A-R peptides, for both CID and HCD fragmentation. The fragmentation efficiency is defined as a predicted peak intensity, normalized by the total sum of peak intensities of the same ion type. Similar to the previous findings (Shao et al., 2014), our model reports significantly higher fragmentation efficiency between [X]-Pro residues (where [X] can be any other residues), for both y- and b- ion types. The model also correctly predicts less efficient fragmentation between [X]-[Z] residue pairs where [X] is a hydrophobic residue. Furthermore, the model also correctly identified an increased fragmentation efficiency for b-ions between His-[Z] pairs.