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OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics Reinert, Knut Kohlbacher, Oliver Gröpl, Clemens Lange, Eva Schulz-Trieglaff, Ole Sturm, Marc Pfeifer, Nico Proteomics C++ Differential expression In the talk we describe the freely available software library OpenMS which is currently under development at the Freie Universität Berlin and the Eberhardt-Karls Universität Tübingen. We give an overview of the goals and problems in differential proteomics with HPLC and then describe in detail the implemented approaches for signal processing, peak detection and data reduction currently employed in OpenMS. After this we describe methods to identify the differential expression of peptides and propose strategies to avoid MS/MS identification of peptides of interest. We give an overview of the capabilities and design principles of OpenMS and demonstrate its ease of use. Finally we describe projects in which OpenMS will be or was already deployed and thereby demonstrate its versatility. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Knut Reinert and Oliver Kohlbacher and Clemens Gröpl and Eva Lange and Ole Schulz-Trieglaff and Marc Sturm and Nico Pfeifer 2006 Is Part Of Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/DagSemProc.05471.13 urn:nbn:de:0030-drops-5463 https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.13 eng https://creativecommons.org/licenses/by/4.0/legalcode