A preparative mass spectrometer system includes an ionizer which converts the mixture into gas phase ions of the molecules in the mixture, and a separator which separates the ions according to their mass to charge ratio or mobility. The separator is a linear ion trap mass analyzer that accumulates the ions based on their mass to charge ratio. A surface is in cooperative relationship with the separator so that the separated molecules are soft landed onto the surface at different locations such that the collected molecules can be stored or further processed/analyzed.