Mass Frontier offers the ability to link generated fragments with a mass spectrum. If you start a generation of fragments and mechanisms from Database Manager, the generated fragments are automatically linked with peaks in spectrum according to their m/z values. So Mass Frontier helps you to explain peaks in spectrum. After a generation, highlighted (“explained“) peaks are displayed in a different color (by default red) in the original mass spectrum. Selecting a highlighted peak reveals all the mechanisms leading to it. In addition, generated fragments (a corresponding Fragments & Mechanisms window must be open) can be assigned automatically to peaks in a spectrum in Database Manager by clicking on the Spectrum Processing button  and choosing the Auto Fragment Annotation of Peaks pop-up menu item.

If an “unexplained“ peak is likely to be an isotopic peak of an “explained“ peak, this is depicted in a third color (by default green). Selecting such a peak reveals all the mechanisms leading to the inferred fragment, which can produce this isotopic profile.

There is one very important issue that should be discussed further. The inability to predict energies and barriers in ionized molecules prevents the prediction of all the peaks in a mass spectrum. In addition, Thus, fragment predictability usually ranges between 50-90%. However, a prominent unexplained peak can be of special value for the interpretation or identification of an unknown. An unexplained peak can indicate a compound-specific mechanism that occurs in molecules with similar structural features, or with a common substructure. There are a number of mechanisms that have only been observed in a specific group of compounds and cannot be applied generally when proposing fragmentation and rearrangement pathways.

If you suspect a compound-specific mechanism of fragment formation, you should verify your assumption by conducting a substructure search and then comparing the explained and unexplained peaks in the spectra retrieved by the substructure search.