The invention relates to a method and instrument for the fragmentation of large molecular
analyte ions, preferably
biopolymer ions, by reactions between multiply charged positive
analyte ions and negative reactant ions in RF
quadrupole ion traps. Some of these reactions involve
electron transfer reactions with subsequent dissociation of the
biopolymer analyte ions, and some involve the loss of a
proton, leading to stable product ions. The invention can use any type of
ion traps, particularly three-dimensional RF
quadrupole ion traps, for the reactions between positive and negative ions. The fragmentation yield can be increased because ions that remain stable as radical cations after transfer of an
electron are further fragmented by collisionally induced fragmentation, forming fragment ions that are typical of
electron transfer, and not those typical of collisionally induced fragmentation. The invention preferentially introduces positive ions and negative ions into the
ion trap sequentially through the same aperture.