Low-mass Fragments and Lost Neutrals

A + 2 of protonated MRFA peptide measured with a resolving power of 100 000 with an orbitrap mass spectrometer. The peaks due to the indicated isotope compositions are clearly separated and measured with correct relative abundances. Redrawn, with permission from Thermo-Finnigan documentation. 

The molecular ion fragments and produces ions and neutrals that are not observed in the spectrum. The mass of the neutral product can be deduced from the difference between the mass of the parent ion and that of the observed ionic fragment. 

One can deduce much information concerning the elemental composition from the masses of the neutrals or of the low-mass fragments. 

In the case of fragments containing only carbon and hydrogen, masses range from 36 (C3) to 43 (C3H7) u for three carbon atoms. For two atoms the limits are 24 and 29 u, for four atoms 48 and 57 u, and for five the minimum is 60 u, for C5, which of course is very unlikely We thus observe that ions or neutrals ranging from 30 to 35 u, for example, must necessarily contain atoms other than carbon and hydrogen. 

Some masses can only have one reasonable formula, such as 20 u, which corresponds only to HF. 

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