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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

wer utility in the Xcalibur software based on the proposed elemental compositions.



Figure 5: The extracted ion chromatograms of the drug intermediate and its three impurities labeled with relative peak areas.

In Figure 6, Mass Frontiers Spectra Manager window is used to display the experimentally acquired MS2 spectrum of the pharmaceutical intermediate before and after correlation with predictions made by the Fragments & Mechanisms. Specifically, the chemical structure of the pharmaceutical intermediate was submitted to the program, which then used known unimolecular decomposition reactions to predict possible MS2 fragment ions. These theoretically predicted MS2 fragment ions were then matched to the experi-mental data. Figure 6 shows that all of the major experimental MS2 peaks were accounted for by the program; substantiating the utility of the Fragments & Mechanisms algorithm for predicting the MS2 spectra of submitted chemical structures.


Figure 6: (a) The experimental MS2 spectrum of the drug intermediate. (b) The same spectrum after correlation with theoretically generated fragment ions. Experimental fragments that were accounted for by the Mass Frontier predictive algorithm are colored in red.



Figure 7: The experimental MS2 spectra of (a) the hydroxychloro impurity (b) the dichloro impurity and (c) the dihydro impurity after correlation with theoretically generated fragment ions. Experimental fragments that were accounted for by the Mass Frontier predictive algorithm are colored in red.

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