Editing Chemical ionization (section)

==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.<ref name=":6" /> This results in significantly less fragmentation than does 70 eV electron ionization (EI).

The following reactions are possible with methane as the reagent gas.

=== Primary ion formation ===

:<chem>CH4{} + e^- -> CH4^{+\bullet}{} + 2e^-</chem>

=== Secondary reagent ions ===

:<chem>CH4{} + CH4^{+\bullet} -> CH5+{} + CH3^{\bullet}</chem>

:<chem>CH4 + CH3^+ -> C2H5+ + H2</chem>

=== Product ion formation ===

:<chem>M + CH5+ -> CH4 + [M + H]+</chem> &nbsp;&nbsp; (protonation)

:<chem>AH + CH3+ -> CH4 + A+</chem> &nbsp;&nbsp; (<chem>H^-</chem> abstraction)

:<chem>M + C2H5+ -> [M + C2H5]+</chem> &nbsp;&nbsp; (adduct formation)

:<chem>A + CH4+ -> CH4 + A+</chem> &nbsp;&nbsp; ([[Charge-exchange ionization|charge exchange]])

If ammonia is the reagent gas,

:<chem>NH3{} + e^- -> NH3^{+\bullet}{} + 2e^-</chem>

:<chem>NH3{} + NH3^{+\bullet} -> NH4+{} + NH2</chem>

:<chem>M + NH4^+ -> MH+ + NH3</chem>

For isobutane as the reagent gas,

:<math chem>\ce{C4H10{} + e^- -> C4H10^{+\bullet}{} + 2e^-} (\ce{ + C3H7+} \text{and other ions}) </math>

:<chem>C3H7^+{} + C4H10^{+\bullet} -> C4H9^+{} + C3H8 </chem>

:<chem>M + C4H9^+ -> MH^+ + C4H8 </chem>

Self chemical ionization is possible if the reagent ion is an ionized form of the analyte.<ref>{{Cite journal | doi = 10.1021/ac00226a011 | title = Chemical ionization in Fourier transform mass spectrometry | year = 1981 |author1=Sahba Ghaderi |author2=P. S. Kulkarni |author3=Edward B. Ledford |author4=Charles L. Wilkins |author5=Michael L. Gross | journal = Analytical Chemistry | volume = 53 | pages = 428–437 | issue = 3}}</ref>