The invention relates to a method and apparatus for the fragmentation of large molecules, especially biopolymers. The invention consists in reacting analyte ions with excited or radical neutral particles, whereby, at least in the case of bombardment of analyte ions with helium atoms from an FAB generator, a new type of fragmentation occurs which strongly resembles fragmentation by electron capture (ECD). The reactions may be performed in magnetic ion traps (ion cyclotron resonance cells, ICR), in RF ion traps according to Wolfgang Paul, in RF ion guides, or in free beams of analyte ions or neutral particles.