A system and method for sample analysis using a portable gas chromatography (GC)-mass spectrometry (MS) is provided. The GC-MS system includes an injector configured to accept a sample containing a mixture of chemicals and release at least part of the sample for a separation by GC, a MEMS GC column with an integrated heater configured to accept and at least partly separate the mixture of chemicals, and a mass analyzer in a vacuum chamber configured to accept and mass-analyze the released separated chemicals. The MEMS GC column with the integrated heater is located mostly inside the MS vacuum chamber.