A method and apparatus for processing ions in mass spectrometry is provided. The apparatus includes an ion processing cell having segmented multipole rods and a means for admitting reactive reagent ions to the cell. Provision for timed sequence control of RF and DC voltages to the segmented multipole rods is included. Processing includes trapping analyte ions and subjecting them to selected reactions with reactive reagent ions and/or physical manipulation of the ions by changing the characteristics of the electric field and/or creating discrete regions in the field.