During the generation of possible fragmentation and rearrangement pathways the Generation of Fragments & Mechanisms window is displayed.

In the Already Generated m/z pane is a combo box that stores m/z values of ions that have already been generated. A list of ions that have been generated can be displayed, by clicking on the combo down-arrow. The total number of ions that have already been generated is displayed next to the combo box.

While a generation is in progress the Reactions Limit bar gives you an approximate indication of how many temporary internal reactions have been generated from a particular structure. Large and structurally complicated molecules can produce enormous number of reactions. Because the generated reactions consume a large amount of memory, there is a limit to the number of temporarily-generated reactions. If the reactions limit is reached the generation will be stopped and a message box appears as a reminder of this fact. Even if the generation is stopped, the fragments and mechanisms generated up to that point will be displayed. The system that generates the fragments and mechanisms is designed in such a way that the fragments that are generated first are the most important. Therefore, when a generation is stopped, the most important fragments will probably already have been generated. However, if you are missing an important fragment, and you assume that it is because the generation was interrupted, you can increase the number of internal reactions in the Reaction Restriction window in the Size tab.

A very important message is displayed in the Info pane “Mass Frontier is a multithreading application, so you can use this program while reactions are being generated.” The multithreading strategy allows more than one task to be performed simultaneously. For example, while reactions are being generated, you can search libraries or analyze your spectra. You can even run two or more generations of fragments and mechanisms at the same time.

The Pause button allows you to temporarily interrupt generation to redirect processing power to other processes that might be running simultaneously in Mass Frontier, or to other Windows applications.

A generation can be stopped by clicking on the Finish button. Fragments, along with their production mechanisms generated up to that point, will be displayed.

The Cancel button can be used for aborting a generation. Sometimes it may take several seconds for the window to disappear after the generation has been aborted.