The primary purpose of library reactions is to create a database of fragmentation and rearrangement mechanisms that can be applied to user provided structures to predict the decomposition pathways occurring in a mass spectrometer. The library mechanisms are a significant extension to the general fragmentation rules which may not cover all the complex processes for a broad spectrum of ionization and ion activation techniques. The usefulness of library mechanisms is the flexibility it gives for altering predicted fragmentation pathways and entering highly specific mechanisms that apply for a limited class of compounds. Since the current version contains around 19,000 reactions, the fragmentation predictability is much higher than if only general rules apply. This is especially true for low energetic experiments such as ESI or APCI that often yield complicated skeletal rearrangements and unusual ring closures.

Any recognized and active mechanism that has been saved into a library serves as a Knowledge Base for the prediction of fragmentation pathways. So, after you have drawn and saved a reaction into any fragmentation library, you can use the mechanism template for prediction fragmentation pathways for any structure that the derived mechanism can be applied to. The range of applicability depends on many factors, but structurally similar compounds with a common ring scaffold usually exhibit identical fragmentation mechanisms.

If a fragmentation reaction was predicted using a library reaction, you can double click on the Lib arrow caption to see the corresponding mechanism. Both template and generated fragmentation mechanisms will be displayed in red in the Fragmentation Library window and the Fragments & Mechanisms window.

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