Gas chromatography is one of the most versatile and general techniques in the analytical toolbox, in terms of the ability to separate, identify and quantify (determine amount or concentration of) chemical compounds. It is possible to analyse samples in gaseous, liquid or solid form, both directly and using various forms of offline sample preparation, such as Soxhlet extraction. In combination with a mass spectrometer as detector (MS or GC-MS in combination) it has the unique ability to identify unknown compounds in the sample (non-target screening), either from a database or through interpretation of the mass spectrum. There are also a variety of additional detectors which can be used depending on the needs of a specific application, the most common are the Flame Ionisation Detector (FID), which is used mainly for hydrocarbons, and the Thermal Conductivity Detector (TCD), which is used mainly for permanent gases.
In general, to identify and quantify a chemical compound in a complex sample, the first step is to separate that compound from everything else in the sample. Gas chromatography essentially separates molecules based on their boiling point in a long separation column, and is often described as a very efficient distillation. This is, however, not entirely correct even if boiling point is an important parameter. To identify a compound once it has been separated the combination of retention time and selectivity of the detector is typically used, where the TCD is probably the least selective and MS the most selective of the common detectors, the choice often depends on the complexity of the sample.
In research and development the combination of gas chromatography and mass spectrometry allows an additional dimension of information, which does not arise from the mass spectrometer alone, but the ability to use standardised conditions in the ion source, which ionises the compounds as they enter the mass spectrometer. When standardised conditions are employed the mass spectra are transferrable between instruments and manufacturers, which allows building of large databases of known compounds which can be used to identify unkowns. Additionally a standardised energy (70 eV) is used so that the molecules partially fragment in the ion source resulting in a predictable fragments related to the chemical structure of the molecule, which allows both elucidation of the structure of the molecule from the fragments found and a highly specific “fingerprint” for matching against a database. The most common commercial database (NIST) in the later versions contain approximately 350 000 such mass spectra of different compounds, which greatly simplifies the work of the chemist, especially identification of unknowns, as in the case of non-target screening.