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If you use the Open Source version in your thesis, please cite it as

OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data, Philip Wenig, Juergen Odermatt, BMC Bioinformatics; 2010, doi:10.1186/1471-2105-11-405

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OpenChrom® is a registered trademark of Lablicate GmbH.