An important aspect of this pipeline is the generation of a detailed processing report with an overview of the effect of each filtering step. This provides insights into metadata deficiencies in a library and the cleaning pipeline's effectiveness. Examples of such processing reports can be found in Table and Table . Another important goal was to increase the reproducibility of library cleaning, harmonization, and processing. Hence, our pipeline automatically creates a YAML file. This YAML file gives a clear humanreadable and computer-readable record of all the performed filter steps and can be used as direct input to rerun a pipeline with exactly the same filters and settings. This facilitates sharing and replication of such mass spectral filtering processes.