Detecting and identifying ions using surface enhanced Raman spectroscopy (SERS) and an ion separation pre-filter, such as an ion spectrometer, are provided. The combination of an ion separator as a pre-filter for SERS provides a highly sensitive detector with very low false alarm rates. Target ions from an ionized sample are identified and separated by the ion separator. The target ions are steered and deposited onto a SERS substrate for Raman spectroscopic analysis with an optical probe. The Raman spectrum is compared with reference spectra and the composition of the sample is identified. The ion current from the target ions can also be measured, preferably concurrently with the Raman spectrum measurement. Types of ion separators include a differential ion mobility spectrometer, an ion mobility spectrometer, or a mass spectrometer.