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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

Fragments & Mechanisms is particularly useful for:

Checking the correlation between a proposed chemical structure and its experimental mass spectrum

Confirming library search assignments

Recognizing structural differences in the spectra of closely related compounds

In addition, Fragments & Mechanisms can simulate MS2 experiments. When a user-specified compound structure is entered, a number of theoretical secondary ion decomposition reactions are generated for comparison with experimental MS2 data. In this study, the simulated fragmentation products of proposed structures were correlated with observed spectra generated from Data Dependent MS2 and used to confirm the structures of three trace-level impurities associated with a key intermediate of a pharmaceutical lead.

Discussion

As part of a recent process evaluation of a key intermediate of a pharmaceutical lead, Eisai Research Institute determined that an extensive structural analysis of these intermediates impurities was necessary before proceeding with the next step. For proprietary reasons, only a partial structure of this compound is shown in Figure 1.

The sample (20 L of a solution containing 100 ng/L of the pharmaceutical intermediate and its impurities) was loaded onto the column and eluted into the mass spectrometer. The LCQ Deca was operated in a Data Dependant MS2 scanning mode, where both full-scan MS and MS2 data were acquired in a single run without pre-specification of MS2 precursor masses. A plot of the total ion current detected by the analysis is given in Figure 2a. A strong signal at m/z 486, corresp
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