Vaporized analyse when carried through the GC column with the help of heated carrier gas the separation occurs in the column. Then the separated components of the mixture will enter into the MS through an interphase. This is followed by ionization, mass analysis and detection of mass-to-charge ratios of ions generated (m/z) from each analyse by the mass spectrometer. The interface works as a bridge connecting the GC and MS. Together with the vacuum pumping system, they lower the pressure to meet the high vacuum requirement of MS. The interface is gas-tight and maintained at low and consistent pressure by pumps. Carrier gases can be removed at this step. With a heater, the interface temperature is kept high (e.g. 50 –350°C) to ensure that the eluted compounds from the GC stay in the gaseous phase and only volatile compounds enter the MS. In GC-MS, the ion source converts gaseous molecules (M(g)) into charged ions (Mn+) by means of electron bombardment or collision/reaction with a reagent gas. Electron ionization (EI) and Chemical ionization (CI) are the main ionization modes used in GC-MS. The characteristics of each ionization method and the processes that occur in the ion source chamber are described in depth in this section. It serves as a guide to understand and select the most suitable ion source for your required analysis. The process of ionisation not only ionise the molecule but also break the molecule into the positive or negative modes2.