Mass Frontier allows the automated prediction of fragments from a user provided structure. If you start the generation of fragments from Database Manager and the active record contains a structure (an MS1 structure for Spectral Tree), the generated fragments are automatically linked with peaks in the spectrum (spectra in the Spectral Tree) according to their m/z values. After a generation, highlighted (“explained“) peaks are displayed in a different color (in red by default) in the original mass spectrum. Clicking on 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 by clicking on the Spectrum Processing button   and choosing the Auto Fragment Annotation of Peaks pop-up menu item.

In addition to automated peak annotation you can also manually assign fragment structure to any peak by clicking on Assign Fragment Structure to Peak button .