Matchms and PubChem cleaned MS/MS dataset from GNPS

<p>Dataset of MS/MS spectra retrieved from GNPS (https://gnps.ucsd.edu) on 25/01/2021, which underwent extensive metadata cleaning.</p> <p>Version v1 contained a bug (missing &quot;NUM PEAKS&quot; parameters), this was corrected in version v2.</p> <p>Metadata was cleaned and processed using matchms (https://github.com/matchms/matchms) and matchmsextras (https://github.com/matchms/matchmsextras). This largely consited of</p> <ul> <li>Empty spectra were removed.</li> <li>Compound names were cleaned</li> <li>charge, adduct, formula, ionmode fields were cleaned and corrected</li> <li>parent mass estimated were added (using precursor mz and adduct information)</li> <li>inchikey, inchi, and SMILES were checked and corrected</li> <li>Spectra which remained without inchi/inchikey/smiles were searched against pubchem based on their mass and name.</li> </ul> <p>This resulted in 210,400 spectra out of which 184,698 are annotated with InChIKey and SMILES and/or InChI.</p> <p>If you use this dataset for your research please cite the following:</p> <ul> <li>GNPS, e.g. [Wang, M. <em>et al.</em> Sharing and community curation of mass spectrometry data with GNPS. <em>Nat. Biotechnol. </em><strong>34</strong>, 828&ndash;837 (2016)]</li> <li>matchms: [ Huber, F. <em>et al.</em> matchms - processing and similarity evaluation of mass spectrometry data. <em>J. Open Source Softw. </em><strong>5</strong>, 2411 (2020) ]</li> <li>PubChem: [ Kim, S. <em>et al.</em> PubChem 2019 update: improved access to chemical data. <em>Nucleic Acids Res. </em><strong>47</strong>, D1102&ndash;D1109 (2019)]</li> </ul> <p>Many thanks!</p>