Ion manipulation systems include ion repulsion by an RF field penetrating through a mesh. Another comprises trapping ions in a symmetric RF field around a mesh. The system uses macroscopic parts, or readily available fine meshes, or miniaturized devices made by MEMS, or flexible PCB methods. One application is ion transfer from gaseous ion sources with focusing at intermediate and elevated gas pressures. Another application is the formation of pulsed ion packets for TOF MS within trap array. Such trapping is preferably accompanied by pulsed switching of RF field and by gas pulses, preferably formed by pulsed vapor desorption. Ion guidance, ion flow manipulation, trapping, preparation of pulsed ion packets, confining ions during fragmentation or exposure to ion to particle reactions and for mass separation are disclosed. Ion chromatography employs an ion passage within a gas flow and through a set of multiple traps with a mass dependent well depth.