The invention generally relates to sample analysis with a miniature mass spectrometer. In certain embodiments, the invention provides methods that involve generating ions of a first analyte and ions of a second analyte. Those ions are transferred through a discontinuous sample introduction interface into a first ion trap of a mass spectrometer in a manner in which the discontinuous sample introduction interface remains open during the transferring. The discontinuous sample introduction interface is closed and the ions are sequentially transferred to a second ion trap of the mass spectrometer where they are sequentially analyzed.