This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.
Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. The sequence is below:
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
From this particular sequence, there are 11 D and Es as well as 11 R and Ks.
