Comprehensive two-dimensional gas chromatography- mass spectrometry (GC × GC-qMS) can provide powerful physical separation, signal enhancement, and spectral identification for analytes in complex samples. Unassigned peaks are commonly presented in the untargeted profile after a single run with EI-MS spectral matching and retention index (RI) confirmation. The procedure proposed in this work can be applied as a general method for suggesting or narrowing down the candidates of unassigned GC × GC-qMS peaks. To begin, peak purity detection and chemometric resolution are employed to acquire pure mass spectra. In addition, the fragmental rules and in-silico spectra from structures are available for annotating certain unassigned peaks with reference spectra that are not observed in commercial databases. Furthermore, the procedure proposed in this work allows for in silico RI calculation by means of random forest (RF) analysis based on the retention data under the same chromatographic conditions. The calculated RIs can aid in analysis when the RI information of peaks of interest is not available in retention data libraries. Using the proposed strategy, certain unassigned peaks can be attributed to sesquiterpene metabolites in an in-house database for Cyperus rotundus.
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