The library cleaning pipeline was also run without the newly added repair functions focused on repairing annotation. When running this pipeline, without these repair functions, a total of 83843 spectra were removed, since they did not have a valid annotation or there was a mismatch between parent mass and annotation. In the library cleaning pipeline only 31758 spectra were removed showing that combined the newly introduced repair functions repaired the metadata of 52084 spectra. The final cleaned GNPS public mass spectral library contains 448.485 curated mass spectra and is available on Zenodo (Niek F. de Jonge, 2023a).