A spectroscopic chemical compound identification system includes a container, a memory, a spectrometer, and a processor. The container receives unknown chemical compound. The memory stores a plurality of spectral signatures corresponding to known chemical compounds. The spectrometer measures a spectral signature of the unknown chemical compound through the container. The processor is connected to the memory and the spectrometer, performs a comparison of the spectral signature with at least one of the plurality of spectral signatures, and determines the identity of the unknown chemical compound from the comparison. The system can be housed in a portable handheld housing. A chemical compound can include a pharmaceutical or controlled substance. The system can be also be used to determine if a pharmaceutical or controlled substance is present within an unknown mixture of chemical compounds.