The　combination　of　infrared　spectroscopy　(IR)　and　ion　mobility　mass　spectrometry　(IM-MS)　has　revealed　that　protein　secondary　structures　are　retained　upon　transformation　from　aqueous　solution　to　the　gas　phase　under　gentle　conditions.　Yet　the　details　about　where　and　how　these　structural　elements　are　embedded　in　the　gas　phase　remain　elusive.　In　this　study,　we　employ　long　time　scale　molecular　dynamics　(MD)　simulations　to　examine　the　extent　to　which　proteins　retain　their　solution　structures　and　the　impact　of　protonation　state　on　the　stability　of　secondary　structures　in　the　gas　phase.　Our　investigation　focuses　on　two　well-studied　proteins,　myoglobin　and　beta-lactoglobulin,　representing　typical　helical　and　beta-sheet　proteins,　respectively.　Our　simulations　accurately　reproduce　the　experimental　collision　cross　section　(CCS)　data　measured　by　IM-MS.　Based　on　accurately　reproducing　previous　experimental　collision　cross　section　data　and　dominant　secondary　structural　species　obtained　from　IM-MS　and　IR,　we　confirm　that　both　proteins　largely　retain　their　native　secondary　structural　components　upon　passing　from　aqueous　solution　to　the　gas　phase.　However,　we　observe　significant　reductions　in　secondary　structure　contents　(19.2　+/-　1.2%　for　myoglobin　and　7.3　+/-　0.6%　for　beta-lactoglobulin)　in　specific　regions　predominantly　composed　of　ionizable　residues.　Further　mechanistic　analysis　suggests　that　alterations　in　protonation　states　of　these　residues　after　phase　transition　induce　changes　in　their　local　interaction　networks　and　backbone　dihedral　angles,　which　potentially　promote　the　unfolding　of　secondary　structures　in　the　gas　phase.　We　anticipate　that　similar　protonation　state　induced　unfolding　may　be　observed　in　other　proteins　possessing　distinct　secondary　structures.　Further　studies　on　a　broader　array　of　proteins　will　be　essential　to　refine　our　understanding　of　protein　structural　behavior　during　the　transition　to　the　gas　phase.