Fragmentation and rearrangement pathways can be generated from any user-supplied structure, including ions and isotopically-labeled compounds. The structure can originate from Structure Editor, Database Manager or from a Fragments & Mechanisms window. Before the generation is performed the program checks the input structure for errors. If any errors are found, a message box will appear informing you about the error(s) and the generation will be aborted.

When you start a generation from Structure Editor, in contrast to the copy function or substructure search, the structure does not have to be selected. The program assumes that the complete structure is intended as input for the generation.

If a generation is started from Database Manager window the program automatically links the generated fragments in the Fragments & Mechanisms window with the corresponding spectrum in the Database Manager window. Peaks are highlighted that have the same m/z value as the generated fragments, in the color that is set in the Spectra Layout dialog window (by default red). Selecting a highlighted peak will reveal all the pathways leading to it.

To start a generation of possible fragmentation and rearrangement pathways:

• Click the button in Structure Editor, Database Manager or Fragments & Mechanisms window.

• Or, make the Structure Editor or Database Manager active and then choose the Tools | Fragments & Mechanisms menu item.

When you start generation Reaction Restriction window pops up to allows you specifying the type of knowledge that should be used for fragmentation.