Cross section distributions of [subP+3H]3+ (left), [subP+2H]2+ (middle), and [subP(3- 11)+2H]2+ (right) and corresponding ions of Pro→Ala analogues, for the purpose of assigning Xxx-Pro peptide bonds as cis or trans. For [subP(3–11)+2H]2+, the top spectrum (A) shows the cross section distribution of [subP(3–11)(P4A)+2H]2+ ions corresponding to subP(3–11)(P4A) produced from incubation of subP(P4A), the middle spectrum (B) shows the cross section distribution of [subP(3–11)(P4A)+2H]2+ from the synthesized subP(3–11)(P4A) peptide, and the bottom spectrum (C) shows the mobility profile of [subP(3–11)+2H]2+ produced during incubation of subP in ethanol at 55 °C after 150 min.