Typical modes of bond cleavages of organic compounds in mass spectrometry are briefly summarized. Although these fragmentation rules can be quite useful for interpreting mass spectra of simple compounds, application to structurally complex molecules that contain multiple hetero atoms such as nitrogen or oxygen becomes increasingly difficult, because the exact location of an unpaired electron or positive or negative charges becomes obscure in precursor ions.

About a decade ago, we proposed “a rule of mass shift,” which correctly predicts the m/z for observed peaks corresponding to singly charged even-electron fragment ions. The basis of the rule postulates that ions observed as peaks in an ordinary mass spectrum should be sufficiently stable to survive during the flight path in a mass spectrometer.

The important recognition is that each atom in a stable ion should be in an ordinary valence state, and no free valence should be allowed. Therefore, if the cleavage of a bond leads to an ion with an unstable structure, some structural changes must take place in order for the ion to be observed in the mass spectrum. Such structural changes can be the addition of hydrogen atom(s) and/or a proton for positive ions, and the addition of a hydrogen atom and/or the elimination of two hydrogen atoms in the case of negative ions. These required structural changes in each case are schematically depicted and discussed in detail.

Two typical examples are shown, in which m/z’s of the observed peaks are correctly predicted. The scope and limitations, as well as the significance of the rule for analyzing fragmentations in organic mass spectrometry are also discussed.

A sheet-like ultraviolet (UV) probe laser is used to investigate the ejection and propagation of ion packets of matrix CHCA, which are produced by matrix-assisted laser desorption and ionization (MALDI). Laser irradiation of the expanding MALDI plume induced photodissociation of the CHCA-related ions, which existed in a sheet-like volume, leading to their absence in their MALDI signal profiles. The MALDI spectra were measured under varying conditions: the temporal delay of the lasers and the distance of the sheet-like probe laser from the MALDI sample surface. It was found that the center of the (CHCA)H⁺ packets were ejected at 46±11 ns after MALDI laser irradiation, while the (CHCA)₂H⁺ packets were ejected at 64±12 ns, regardless of the magnitude of acceleration static high-voltage in 3.5–5.5 kV. This suggests that (CHCA)₂H⁺ is formed by a proton transfer reaction from (CHCA)H⁺ to (CHCA)₂ in the heated condensed phase and/or near the surface. This study represents the first experimental determination of ion ejection time in the MALDI process, which is also applicable to other species in the MALDI plume.