Atmospheric Pressure Ionization and Fragmentation

The API methods, which have vastly extended the range of mass spectrometry, produce simple spectra that often exhibit only the molecular mass of the analyte with no (or minimal) fragmentation, and little structural information. Methods were required to induce fragmentation and thereby increase the information content of API spectra. The techniques developed, often tailored to specific objectives, control the amount of energy added to the analytes so that the fragmentation is directed to certain chemical bonds. This is particularly relevant for the analysis of biopolymers where the fragmentation takes place at specific points in the structure, e.g., the peptide bond, and provides sequence and other structural information. 

A distinction is made between fragmentation inside the ion source and those occurring in other locations. Although the processes taking place in MS/MS are still fragmentations, specific names are used to indicate the type of processes, e.g., collision-induced dissociation (Section 3.3.2.1), infrared multiphoton dissociation (Section 3.3.2.2), electron transfer dissociation and electron capture dissociation (Section 3.3.2.3), as well as the more specialized photodissociation and surface-induced dissociation (Section 3.3.2.4). 

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