Fig. 2: Workflow to establish the structure of CID MSn fragment ions. | Communications Chemistry

Fig. 2: Workflow to establish the structure of CID MSn fragment ions.

From: A spectroscopic test suggests that fragment ion structure annotations in MS/MS libraries are frequently incorrect

Fig. 2

The MSn fragment ion of interest is generated by CID and isolated in the ion trap mass spectrometer, where its IRIS spectrum is recorded. DFT geometry optimizations and vibrational frequency calculations are performed for the structures listed in MS/MS libraries as well as for alternative structures suggested by chemical intuition. The structure providing the predicted spectrum with the best match to experiment is annotated as the actual MSn fragment ion structure. Based on this identification, we propose plausible reaction paths from precursor to product ion.

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