Method and apparatus for chromatographic high field asymmetric waveform ion mobility spectrometry, including a gas chromatographic analyzer section intimately coupled with an ionization section, an ion filter section, and an ion detection section, in which the sample compounds are at least somewhat separated prior to ionization, and ion filtering proceeds in a planar chamber under influence of high field asymmetric periodic signals, with detection integrated into the flow path, for producing accurate, real-time, orthogonal data for identification of a broad range of chemical compounds.