The Sizes page allows the user to limit the size and complexity of a reaction pathway generation. The Reaction Steps Max Number box gives the number of cascaded fragment reactions. Increasing this number could exponentially increase the number of fragments produced for a given reaction path. Generally, this number should be kept small, and if additional fragments need to be generated, individual fragments can be selected by the user and used as starting points for additional reactions.

Large and structurally complicated molecules can produce an enormous number of reactions. Because generated reactions take up a large amount of memory, the number of temporarily generated reactions is limited. 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. If the reactions limit is reached, the generation will be stopped, and a message box will appear as a reminder of this fact. Even if the generation is stopped, the fragments and mechanisms generated up to that point will be displayed. 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 believe this is due to the generation being interrupted, you can increase the number of internal reactions in the Reactions Limit box.

The m/z precision of calculated fragments can be set in the Precision Settings. The isobaric differentiation of calculated fragments can be set in the Resolution Settings.