A method and apparatus are provided for operating a linear ion trap. A linear ion trap configuration is provided that allows for increased versatility in functions compared to a conventional three-sectioned linear ion trap. In operation, the linear ion trap provides multiple segments, the segments spatially portioning an initial population of ions into at least a first and a second ion population. Each segment is effectively independent and ions corresponding to the first ion population are able to be manipulated independently from ions corresponding to ions corresponding to the second ion population; the ions having been generated by an ion source under the same conditions. The ions can then be expelled from the ion trap.