In almost all cases incorrect
Various algorithms predict in silico MS/MS spectra to resolve the molecular structure of unknowns found in mass spectrometric analyses. In the predicted MS/MS spectrum, structure annotations of the MS/MS fragment ions may be shown. Although they are not relevant in the matching of experimental and predicted MS/MS spectra, they give insight into the underlying algorithm and are sometimes suggested to be useful in the analysis of deeper-level MSn spectra.
But the question then remains how reliable these algorithms predict these structural annotations. A spectroscopic study of (a small sample set of) these fragment ions at the FELIX Laboratory now suggests that the structure annotation of MS/MS fragment ions in commonly used libraries are in almost all cases incorrect. Hence, although the prediction of the MS/MS spectrum may be useful, the predicted molecular structures of fragment ions should not be used to serve any purpose in the interpretation of MS/MS spectra.
Just published in Communications Chemistry: https://rdcu.be/dyBLf
