GC columns represent the stationary phase and separation tool of a gas chromatography analysis. Using extensive commercially available libraries of mass spectra, unknown compounds and target analytes can be identified and quantified. When a complex sample is separated by GC-MS, it will produce many different peaks in the gas chromatogram and each peak generates a unique mass spectrum used for compound identification. Peak areas, meanwhile, are proportional to the quantity of the corresponding compound. The final steps of the process involve ion detection and analysis, with fragmented ions appearing as a function of their m/z ratios. GC-MS data acquisition can be performed in either full scan mode, to cover either a wide range of m/z ratios, or selected ion monitoring (SIM) mode, to gather data for specific masses of interest. It is here that ions are separated based on their different mass-to-charge ( m/z) ratios. Ionized molecules and fragments are then accelerated through the instrument’s mass analyzer, which quite often is a quadrupole or ion trap. Once the components leave the GC column, they are ionized and fragmented by the mass spectrometer using electron or chemical ionization sources.
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