Once reaction-generating process has finished, a Fragments & Mechanisms window is displayed.

A Fragments & Mechanism window allows the display of either complete mechanisms of ion-decomposition reactions, or of resulting fragments only. To display the desired mechanism, or fragment for a particular m/z value, choose the appropriate m/z tab. If you do not like the tab control you can replace it with a combo box in the Options | Mechanism Layout dialog window.

A Fragments & Mechanism window contains two Copy buttons. The first one is designed for the copying of mechanisms in graphic format (Enhanced Windows Metafile). The second one is for the copying of a selected fragment. If you copy a fragment, this can be pasted to Structure Editor, Database Manager in Mass Frontier or to any Windows application.

Several possible isobaric fragments can be generated for a particular m/z value. If more then one fragment is generated for a m/z value, a hand pointer with the caption “Select possible fragments with m/z xy” will move from right to left to draw your attention to this fact. The isobaric fragments, with their corresponding mechanisms, can be displayed by clicking the numbered buttons next to the hand pointer.

The fragments are sorted according to the simplicity of their production mechanism. So, fragment No.1 is produced by the simplest (shortest) mechanism. The isobaric fragments are usually isomers of the same fragments with a different charge, radical or, p-bond location.