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OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics

Authors Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, Eva Lange, Ole Schulz-Trieglaff, Marc Sturm, Nico Pfeifer



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Knut Reinert
Oliver Kohlbacher
Clemens Gröpl
Eva Lange
Ole Schulz-Trieglaff
Marc Sturm
Nico Pfeifer

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Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, Eva Lange, Ole Schulz-Trieglaff, Marc Sturm, and Nico Pfeifer. OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
https://doi.org/10.4230/DagSemProc.05471.13

Abstract

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.
Keywords
  • Proteomics
  • C++
  • Differential expression

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