Extended Data Fig. 5: Internal fragments generated by the collisional activation of native protein complexes share common terminal fragmentation sites.

a, Counts of internal fragments sharing specific N- or C- terminal fragmentation sites observed upon collisional activation of the dimeric ACE2 complex. Counts for each set of internal fragments sharing a N- (upper) or C-terminal (lower) fragmentation site are presented for the ‘true’ target set of theoretical ions (blue), as well as for an example set of decoy ions generated by adding the mass of acetate (42.0105 Da) to each theoretical ion (grey). Across all examined collision energies, there are sets of internal fragments with a shared fragmentation site that were larger in population than anticipated when assuming random matching. Sets of internal fragments with a shared fragmentation site that were deemed statistically significant (expectation value < 0.01) were selected for assignment (purple marks). b, Distribution of the assigned internal fragments along the length of ACE2. Horizontal lines represent individual sequence ions, with ions generated at HCD 150 V shown in grey and at HCD 200 V shown in black. Internal fragments are formed from localized areas, and are primarily generated by cleavage at high-propensity fragmentation sites (for example, D|P fragments). c, Number of statistically significant (expectation value < 0.01) sets of internal fragments with a common terminal fragmentation site identified at increasing HCD acceleration voltages. d, Number of internal fragments assigned at increasing HCD acceleration voltages.