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FELIX reveals that structure annotations in MS/MS libraries are frequently incorrect

Ever wondered how realistic the structure annotations of MS/MS fragment ion peaks are that you may encounter in common MS libraries?

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:

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

Lara van Tetering, Sylvia Spies, Quirine D. K. Wildeman, Kas J. Houthuijs, Rianne E. van Outersterp, Jonathan Martens, Ron A. Wevers, David S. Wishart, Giel Berden & Jos Oomens 

Communications Chemistry, volume 7, Article number: 30 (2024)