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 . the reactions may be performed in magnetic ion traps , in rf ion traps according to wolfgang paul , in rf ion guides , or in free beams of analyte ions or neutral particles .