The pipeline combines various filter functions to harmonize metadata, derive missing metadata, repair inaccurate metadata, or discard spectra with incorrect annotations. Basic validation of annotations is obtained by enforcing consistency across metadata. Rather than simply discarding all mass spectra with mismatching metadata, our pipeline automatically corrects common errors. For instance, the compound's mass in the annotation should match the parent mass, precursor m/z, and adduct type that is provided. Repairing these common errors reduces the number of spectra that are deleted, retaining a larger and more diverse spectral library. To reduce the risk of repairing metadata of spectra with incorrect annotations, the pipeline only repairs changes if they are supported by multiple sources of metadata. For instance, the SMILES is only derived from PubChem based on a compound name if it actually matches the given parent mass.