Matchms and PubChem cleaned MS/MS dataset from GNPS

Dataset of MS/MS spectra retrieved from GNPS (https://gnps.ucsd.edu) on 25/01/2021, which underwent extensive metadata cleaning.

Metadata was cleaned and processed using matchms (https://github.com/matchms/matchms) and matchmsextras (https://github.com/matchms/matchmsextras). This largely consited of

Empty spectra were removed.

Compound names were cleaned

charge, adduct, formula, ionmode fields were cleaned and corrected

parent mass estimated were added (using precursor mz and adduct information)

inchikey, inchi, and SMILES were checked and corrected

Spectra which remained without inchi/inchikey/smiles were searched against pubchem based on their mass and name.

This resulted in 210,407 spectra out of which 184,698 are annotated with InChIKey and SMILES and/or InChI.

If you use this dataset for your research please cite the following:

GNPS, e.g. [Wang, M. et al. Sharing and community curation of mass spectrometry data with GNPS. Nat. Biotechnol. 34, 828–837 (2016)]

matchms: [ Huber, F. et al. matchms - processing and similarity evaluation of mass spectrometry data. J. Open Source Softw. 5, 2411 (2020) ]

PubChem: [ Kim, S. et al. PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 47, D1102–D1109 (2019)]

Many thanks!