Thermal Degradation Versus Ion Fragmentation

Processes such as decarbonylation, decarboxylation, elimination of water, and several other reactions may also occur prior to ionization, i.e., as non-mass spectral reactions, typically as a result of thermal degradation upon heating of the sample to enforce evaporation. In such a case, the mass spectrum obtained is not that of the analyte itself, but of its decomposition product(s). Sometimes, those thermal reactions are difficult to recognize, because the same neutral loss may also occur by a true mass spectral fragmentation of the corresponding molecular ion. 

In even more disadvantageous circumstances, the thermal decomposition does not yield a single defined product, but a complex mixture that results in almost useless spectra, e.g., in case of highly polar natural products such as saccharides, nucleotides, and peptides or in case of ionic compounds such as organic salts or metal complexes. 

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