FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
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Updated: Jun 17, 2026

Natural Product Discovery with LC-MS/MS Diagnostic Fragmentation Filtering: Application for Microcystin Analysis
Published on: May 31, 2019
Harald Barsnes1, Ingvar Eidhammer, Lennart Martens
1Department of Informatics, University of Bergen, Bergen, Norway. Harald.Barsnes@ii.uib.no
Abstract:
A thorough understanding of the fragmentation processes in MS/MS can be a powerful tool in assessing the resulting peptide and protein identifications. We here present the freely available, open-source FragmentationAnalyzer tool (http://fragmentation-analyzer.googlecode.com) that makes it straightforward to analyze large MS/MS data sets for specific types of identified peptides, using a common set of peptide properties. This enables the detection of fragmentation pattern nuances related to specific instruments or due to the presence of post-translational modifications.
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