Figure 2. Orphan isotopologue contamination and MS/MS spectrum prediction.

(a) An orphan carbon-13 isotopologue can cause MS/MS contamination if the M+0 parent of a contaminating compound (red) is excluded from the isolation window (gray) but the M+1 carbon-¹³ peak is not. Such chimeric MS/MS spectra cannot be deconvolved by considering only database spectra and will severely impact the ability to identify the targeted precursor (blue). (b-c) Schematic of predicting the MS/MS spectrum of an M+1 isotopologue arising from naturally occurring carbon-13. (b) First, based on the chemical formula of the precursor ion, all possible subformulas are enumerated, and the m/z of each subformula is computed. Then, for each observed fragment, the possible subformulas are assigned and the mean number of carbon atoms for all possible subformulas of each fragment are computed. (c) Using the computed number of carbons in each fragment, the intensity of each fragment in the M+1 spectrum is computed by distributing the intensity of the M+0 fragment ions according to the number of carbons in each fragment. All carbon atoms are equally likely to be carbon-13, thus for a seven-carbon fragment and an eight-carbon precursor, there is a 7/8 probability that the carbon-13 is retained in the fragment and a 1/8 probability that it is removed as a neutral loss. Carbon atoms are represented by gray and red circles for carbon-12 and carbon-13, respectively.