Practical Approaches to Interpret Mass Spectra

So you have a mass spectrum of an organic compound in your hands. How should you start the process of identification By this time it is very useful to have all available information on the sample. Any information may be relevant (method of synthesis and isolation, the nature of precursors and solvents, the presence of impurities, etc.). Sometimes even knowing what was synthesized in the same flask earlier may be of crucial importance for the final decision. 

First of all it is helpful to check the presence of similar spectra in the available spectral databases. Ideally the task may be completely resolved at this stage. The library search may help to refer the sample to a certain class of organic compounds, to get some clues on the presence of heteroatoms and functional groups. 

Further, one should pay attention to the general appearance of the spectrum (parameters of the mass spectrometer, the most intense peaks, and characteristic groups of peaks). Thus, if there are many peaks of fragment ions, while their intensity increases toward the low m/z values, the sample most probably belongs to the aliphatic compounds. On the contrary, rare intense peaks indicate the aromatic nature of the sample. You should start the detailed interpretation with identification of the molecular ion peak. 

One can get an enormous amount of information from studying the region of the molecular ion in a mass spectrum. The mass of M+ is the molecular mass of the analyte. The ratio of the isotopic peaks (see below) allows one to roughly establish the elemental composition, while accurate mass measurements using high resolution mass spectrometry give exact elemental composition. The relative intensity of the M+ peak 

Unfortunately many compounds do not have a peak for their M+ in electron ionization mass spectra, as it is unstable. That is why it is of primary importance to be able to identify M+ correctly. There are four necessary but not sufficient conditions to name an ion peak molecular. If at least one of these conditions fails the ion is not molecular. If all four statements are fulfilled, the ion can be molecular. 

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