The first crucial step during the cleanup of metadata is the standardization of chemical structures, often provided by sellers of compound libraries or accessed from public compound databases. The Python script presented here is based on the ChEMBL structure standardizer, adding a step to remove salts from parent compounds. The majority of salts, such as tartrates, are most likely dissociated in solution before MS analysis and only later form ion adducts or clusters during ionization. The cleaned structure is then converted into canonical or isomeric SMILES, InChI, and InChIKey strings, and its exact monoisotopic neutral mass is calculated. This is important for the automatic library generation workflow, which annotates and extracts spectra based on their metadata. For the metadata, ion adducts and their expected m/z are irrelevant because they are computed in mzmine.