Thousands of per-and polyfluoroalkyl substances (PFAS) exist in the environment and pose a potential health hazard. Suspect and non-target screening with liquid chromatography (LC) high-resolution tandem mass spectrometry (HRMS/MS) can be used for comprehensive characterization of PFAS. To date no automated open source PFAS data analysis software exists to mine these extensive datasets. We introduce FluoroMatch, which automates file conversion, chromatographic peak picking, blank feature filtering, PFAS annotation based on precursor and fragment masses, and annotation ranking. The software library currently contains ~7,000 PFAS fragmentation patterns based on rules derived from standards and literature and the software This document is the postprint version of an article published in