thumb|A schematic diagram of chemical ionization source
Chemical ionization (CI) is a soft ionization technique used in mass spectrometry. This was first introduced by Burnaby Munson and Frank H. Field in 1966. This technique is a branch of gaseous ion-molecule chemistry. are ionized by electron ionization to form reagent ions, which subsequently react with analyte molecules in the gas phase to create analyte ions for analysis by mass spectrometry. Negative chemical ionization (NCI), charge-exchange chemical ionization, atmospheric-pressure chemical ionization (APCI) and atmospheric pressure photoionization (APPI) are some of the common variants of the technique. CI mass spectrometry finds general application in the identification, structure elucidation and quantitation of organic compounds as well as some utility in biochemical analysis. CI is thus useful as an alternative technique in cases where EI produces excessive fragmentation of the analyte, causing the molecular-ion peak to be weak or completely absent.
Instrumentation
The CI source design for a mass spectrometer is very similar to that of the EI source. To facilitate the reactions between the ions and molecules, the chamber is kept relatively gas tight at a pressure of about 1 torr. Electrons are produced externally to the source volume (at a lower pressure of 10<sup>−4</sup> torr so that they penetrate to at least the centre of the box.
Mechanism
A CI experiment involves the use of gas phase acid-base reactions in the chamber. Some common reagent gases include: methane, ammonia, water and isobutane. Inside the ion source, the reagent gas is present in large excess compared to the analyte. Electrons entering the source will mainly ionize the reagent gas because it is in large excess compared to the analyte. The primary reagent ions then undergo secondary ion/molecule reactions (as below) to produce more stable reagent ions which ultimately collide and react with the lower concentration analyte molecules to form product ions. The collisions between reagent ions and analyte molecules occur at close to thermal energies, so that the energy available to fragment the analyte ions is limited to the exothermicity of the ion-molecule reaction. For a proton transfer reaction, this is just the difference in proton affinity between the neutral reagent molecule and the neutral analyte molecule.
Advantages and limitations
One of the main advantages of CI over EI is the reduced fragmentation as noted above, which for more fragile molecules, results in a peak in the mass spectrum indicative of the molecular weight of the analyte. This proves to be a particular advantage for biological applications where EI often does not yield useful molecular ions in the spectrum. As with EI, the method is limited to compounds that can be vapourized in the ion source. The lower degree of fragmentation can be a disadvantage in that less structural information is provided. Additionally, the degree of fragmentation and therefore the mass spectrum, can be sensitive to source conditions such as pressure, temperature, and the presence of impurities (such as water vapour) in the source. Because of this lack of reproducibility, libraries of CI spectra have not been generated for compound identification. Almost all neutral analytes can form positive ions through the reactions described above.
In order to see a response by negative chemical ionization (NCI, also NICI), the analyte must be capable of producing a negative ion (stabilize a negative charge) for example by electron capture ionization. Because not all analytes can do this, using NCI provides a certain degree of selectivity that is not available with other, more universal ionization techniques (EI, PCI). NCI can be used for the analysis of compounds containing acidic groups or electronegative elements (especially halogens).
Because of the high electronegativity of halogen atoms, NCI is a common choice for their analysis. This includes many groups of compounds, such as PCBs,