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Preservation of protein conformation upon transfer into the gas phase is key for structure determination of free single molecules, for example using X‐ray free‐electron lasers. In the gas phase, the helicity of melittin decreases strongly as the protein's protonation state increases. We demonstrate the sensitivity of soft X‐ray spectroscopy to the gas‐phase structure of melittin cations ([melittin+ q H]  q + ,  q =2–4) in a cryogenic linear radiofrequency ion trap. With increasing helicity, we observe a decrease of the dominating carbon 1 s–π* transition in the amide C=O bonds for non‐dissociative single ionization and an increase for non‐dissociative double ionization. As the underlying mechanism we identify inelastic electron scattering. Using an independent atom model, we show that the more compact nature of the helical protein conformation substantially increases the probability for off‐site intramolecular ionization by inelastic Auger electron scattering.

Soft X‐ray Spectroscopy as a Probe for Gas‐Phase Protein Structure: Electron Impact Ionization from Within