Ion mobility resolved photo‐fragmentation to discriminate protomers.

Rationale: Among the sources of structural diversity in biomolecular ions, the co‐existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas‐phase data. Methods: We investigated the sensitivity of gas‐phase photo‐fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo‐fragmentation measurements on mobility‐selected ions. All results were interpreted based on molecular dynamics simulations. Results: We show that protonation can significantly affect the photo‐fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo‐fragmentation yields in relation with different protonation patterns. Conclusions: We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo‐fragmentation and IMS can help to identify the signature of protomer co‐existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes. [ABSTRACT FROM AUTHOR]