GC/MS instruments offer two ionization techniques: electron ionization (EI) and chemical ionization (CI).
EI is commonly used because it is simple and reproducible. The fragmentation pattern is effectively determined by the energy of the impacting electrons alone (electron energy, measured in eV). Different types of mass spectrometers that use EI can produce virtually identical spectra as long as they have the same electron energy.
NOTE
You can purchase the National Institute of Science and Technology™ (NIST) Mass Spectral Search application from the NIST. Thermo Fisher Scientific provides local versions of the NIST application and its libraries with the Xcalibur™ data system.
CI offers a softer method of forming ions. In CI, a controlled flow of a reagent gas, commonly ammonia, methane, or isobutane, is introduced into the area where ionization occurs (the ion source). Energetic electrons that pass through the source ionize the neutral molecules, like in EI. The ions can collide with the gaseous neutral molecules, causing hydrogen transfer. This process is repeated when the reagent gas ions collide with neutral analyte molecules.
CI usually produces protonated molecules, generally at a mass that is one unit greater than the molecular mass of the compound. CI causes significantly less fragmentation than EI. Depending on your choice of reagent gas, adduct ions can form during CI. For example, when you use ammonia as the reagent gas, M+NH4 is a typical adduct ion.
Under certain conditions, CI produces negative molecular ions; such ions result from electron capture. The sensitivity of negative-ion CI for certain classes of compounds (those containing double bonds, sulfur, phosphorus, chlorine, or bromine) can be orders of magnitude greater than those of positive-ion CI or EI modes for the same compounds.