You can specify the type of Knowledge Base the expert system uses for the prediction of fragmentation pathways in the Base group box in the Reaction Restrictions window. The options are: General Fragmentation Rules, Fragmentation Library or both together.

If you choose the Fragmentation Library, you can select which library should be used from the list of libraries. Please note that the preinstalled HighChem Fragmentation Library™ contains around 19,000 mechanisms, and so calculation times will be significantly longer when it is used.

There are four options connected with the Fragmentation Library knowledge base. Since some mechanisms of small fragments can fit to virtually every user provided structure and can generate an immense number of useless fragments, there is an option available to deactivate a record in the Fragmentation Library window. To make use of this option, the Active Record Only option in the Reaction Restriction window must be checked. If this is not done, all mechanisms from the selected libraries will be considered by the expert system.

If a neutral molecule is provided, Mass Frontier automatically simulates the ionization process according to the selected ionization mode in the Ionization & Cleavage tab. However, if you want to disable this automatic simulation and use a different ionization site by adding an ionization mechanism to the library, select the Library Ionization Only check box.

As some fragmentation library mechanisms follow general fragmentation rules, you can speed up the generation by enabling General Fragmentation Rules in the Knowledge Base group and disabling general fragmentation rules in Fragmentation Library Options group in the Ignore General Frag. Rules in the Library Reaction check box.

Mass Frontier allows you to work with structures with an unspecified charge site in the fragmentation library or in the starting structure. This is a very convenient feature, but it has one significant disadvantage - it dramatically slows the generation process. If an unspecified charge site is used, the expert system must consider a huge number of combinations for every step. Therefore, if possible we advise that you avoid using unspecified charge sites in the fragmentation library. To exclude mechanisms in the fragmentation library that contain unspecified charge sites from the generation process, check the Charge Localization Concept Only check box.