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Mass spectrometry data is at the heart of numerable applications in the biomedical and life sciences. With growing use of high throughput techniques researchers need to analyse larger and more complex datasets. In particular through joint effort in the research community, fragmentation mass spectrometry datasets are growing in size and number. Matchms is an open-access Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run andoi:10.1101/2020.08.06.239244 fatcat:folnxbg2t5aqhf32pcf3mln5b4