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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