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

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

05471.ReinertKnut.ExtAbstract.546.pdf (0.2 MB)


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.

BibTeX - Entry

  author =	{Knut Reinert and Oliver Kohlbacher and Clemens Gr{\"o}pl and Eva Lange and Ole Schulz-Trieglaff and Marc Sturm and Nico Pfeifer},
  title =	{OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics},
  booktitle =	{Computational Proteomics},
  year =	{2006},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  number =	{05471},
  series =	{Dagstuhl Seminar Proceedings},
  ISSN =	{1862-4405},
  publisher =	{Internationales Begegnungs- und Forschungszentrum f{\"u}r Informatik (IBFI), Schloss Dagstuhl, Germany},
  address =	{Dagstuhl, Germany},
  URL =		{},
  annote =	{Keywords: Proteomics, C++, Differential expression}

Keywords: Proteomics, C++, Differential expression
Collection: 05471 - Computational Proteomics
Issue Date: 2006
Date of publication: 18.09.2006

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