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Analyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using ,,, an LCQ Deca Ion Trap Mass Spectrometer and the Mass Frontier ,,, Software Package

7 shows the experimental MS2 spectra of the three impurities after correlation with the fragment ions predicted by Mass Frontiers Fragments & Mechanisms module. Mass Frontiers predictions were based on the chemical structures proposed for each of the three impurities displayed in Figure 3. As in Figure 6, the experimental MS2 peaks that corresponded to fragment ions predicted by Mass Frontier are colored in red. The observation that all of the major peaks in the experimental MS2 spectra of the impurities are colored red clearly supports the validity of the proposed structures.

Table 1 summarizes the results of the correlation between Mass Frontiers fragmentation predictions and the experimental MS2 spectra that are used to verify the structures proposed for the impurities in Figure 3. In order to understand how this is done, it is important to recognize that except for the substitution site (colored in red in Figures 1 and 3), the proposed structures of the drug intermediate and the three impurities are identical. Therefore, if the experimental MS2 spectra of the four compounds each possess a fragment ion at m/z values that Mass Frontier assigns to the same mechanism of formation if the structures proposed for the three impurities are correct:

The fragment ion should have the same m/z value in all four experimental MS2 spectra if the Mass Frontier predicted mechanism of formation produces a fragment structure that does not contain the substitution site.

The fragment ion should have experimental m/z values differing by the mass of the substituents if the Mass Frontier predicted mechanism of formation produces a fragment structure that does contain the substitution site (i.e. if the fragment ion has a m/z value of M in the drug intermediates exper
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