Overall, our mass spectral library cleaning pipeline aims to simplify library cleaning and making the process reproducible, resulting in higher-quality spectral libraries. The ease of use combined with the flexibility also allows for future development that can further improve and standardize current practices in mass spectrometry-based metabolomics. Our pipeline is expected to improve the quality of public mass spectral libraries and thereby improve the annotation results of library matching and analogue searching, as well as the future performance of machine learning models.