Determination of the Structure of the Analyte:

You know that the molecular ion obtained in the course of ionisation in the ion source is highly energetic and undergoes fragmentation. In the process of fragmentation the molecular ion loses free radicals or small neutral molecules to give smaller fragments. The fragmentation does not occur randomly instead take place in a way so as to give the stable fragments. The features fragments acquired in the mass spectrum of a compound can provide important leads into its structure. Detailed studies on the mechanism of fragmentation and characteristic fragments of different classes of organic compounds have led to certain general rules which can be used to decipher the structure of an organic compound from its mass spectrum.

A detailed account of the fragmentation of different types of functional groups is beyond the scope of this course. However, let us take up some common fragmentation patterns.