As an example the newly developed pipeline was run on a current version of the GNPS library. The public GNPS library was downloaded on 21-08-2023 (GNPS Library, 2023). We note that we selected the no propagated version to only include experimentally derived mass spectra and annotations. We did run two pipelines with different settings on the GNPS library. For the first pipeline the default settings in the library cleaning pipeline were used and for the second run we used the library cleaning pipeline, without any of the new repair annotation function, to illustrate the effect of these new filters. The cleaned library, the scripts and YAML file with the filters and settings can be found on Zenodo . Matchms version 0.24.0 was used to run these pipelines.