Native　electrospray　ionization/ion　mobility-mass　spectrometry　(ESI/IM-MS)　allows　an　accurate　determination　of　low-resolution　structural　features　of　proteins.　Yet,　the　presence　of　proton　dynamics,　observed　already　by　us　for　DNA　in　the　gas　phase,　and　its　impact　on　protein　structural　determinants,　have　not　been　investigated　so　far.　Here,　we　address　this　issue　by　a　multistep　simulation　strategy　on　a　pharmacologically　relevant　peptide,　the　N-terminal　residues　of　amyloid-β　peptide　(Aβ(1-16)).　Our　calculations　reproduce　the　experimental　maximum　charge　state　from　ESI-MS　and　are　also　in　fair　agreement　with　collision　cross　section　(CCS)　data　measured　here　by　ESI/IM-MS.　Although　the　main　structural　features　are　preserved,　subtle　conformational　changes　do　take　place　in　the　first　∼0.1　ms　of　dynamics.　In　addition,　intramolecular　proton　dynamics　processes　occur　on　the　picosecond-time　scale　in　the　gas　phase　as　emerging　from　quantum　mechanics/molecular　mechanics　(QM/MM)　simulations　at　the　B3LYP　level　of　theory.　We　conclude　that　proton　transfer　phenomena　do　occur　frequently　during　fly　time　in　ESI-MS　experiments　(typically　on　the　millisecond　time　scale).　However,　the　structural　changes　associated　with　the　process　do　not　significantly　affect　the　structural　determinants.　©　2017　American　Chemical　Society.