Dataset of MS/MS spectra retrieved from GNPS (https://gnps.ucsd.edu) on 25/01/2021, which underwent extensive metadata cleaning. Version v1 contained a bug (missing "NUM PEAKS" parameters), this was corrected in version v2. 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 210,400 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!