Abstract: A portable analytical grade mass spectrometer system contained in a single enclosure is disclosed for use in analyzing atmospheric, water, soil, drugs, explosives and other substances and includes a gas chromatograph and a mass analyzer assembly enclosed within a vacuum housing, a vacuum pump, and an on-board computer such that an operator, by means of an attached keyboard, can input data and information, and input a sample to be analyzed, and thereby operate the miniaturized mass spectrometer system.