OpenMS: a flexible open-source software platform for mass spectrometry data analysis

doi:10.1038/nmeth.3959

. 2016 Aug 30;13(9):741-8.

doi: 10.1038/nmeth.3959.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Hannes L Röst^{1

2}, Timo Sachsenberg^{3

4}, Stephan Aiche⁵, Chris Bielow^{6

7}, Hendrik Weisser⁸, Fabian Aicheler^{3

4}, Sandro Andreotti⁵, Hans-Christian Ehrlich⁵, Petra Gutenbrunner⁸, Erhan Kenar^{3

4

9}, Xiao Liang¹⁰, Sven Nahnsen⁹, Lars Nilse¹¹, Julianus Pfeuffer^{3

4}, George Rosenberger¹, Marc Rurik^{3

4}, Uwe Schmitt¹², Johannes Veit^{3

4}, Mathias Walzer^{3

4}, David Wojnar⁹, Witold E Wolski^{1

13}, Oliver Schilling^{11

14}, Jyoti S Choudhary⁸, Lars Malmström^{1

15}, Ruedi Aebersold^{1

16}, Knut Reinert^{5

17}, Oliver Kohlbacher^{3

4

9

18

19}

Affiliations

¹ Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
² Department of Genetics, Stanford University, Stanford, California, USA.
³ Department of Computer Science, University of Tübingen, Tübingen, Germany.
⁴ Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
⁵ Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
⁶ Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.
⁷ Metabolomics Core Facility, Berlin Institute of Health, Berlin, Germany.
⁸ Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK.
⁹ Quantitative Biology Center, University of Tübingen, Tübingen, Germany.
¹⁰ International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC), Berlin, Germany.
¹¹ Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
¹² ID Scientific IT Services, ETH Zurich, Zurich, Switzerland.
¹³ Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland.
¹⁴ BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
¹⁵ S3IT, University of Zurich, Zurich, Switzerland.
¹⁶ Faculty of Science, University of Zurich, Zurich, Switzerland.
¹⁷ Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹⁸ Faculty of Medicine, University of Tübingen, Tübingen, Germany.
¹⁹ Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany.

PMID: 27575624
DOI: 10.1038/nmeth.3959

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Hannes L Röst et al. Nat Methods. 2016.

. 2016 Aug 30;13(9):741-8.

doi: 10.1038/nmeth.3959.

Authors

Affiliations

¹ Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
² Department of Genetics, Stanford University, Stanford, California, USA.
³ Department of Computer Science, University of Tübingen, Tübingen, Germany.
⁴ Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
⁵ Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
⁶ Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.
⁷ Metabolomics Core Facility, Berlin Institute of Health, Berlin, Germany.
⁸ Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK.
⁹ Quantitative Biology Center, University of Tübingen, Tübingen, Germany.
¹⁰ International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC), Berlin, Germany.
¹¹ Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
¹² ID Scientific IT Services, ETH Zurich, Zurich, Switzerland.
¹³ Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland.
¹⁴ BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
¹⁵ S3IT, University of Zurich, Zurich, Switzerland.
¹⁶ Faculty of Science, University of Zurich, Zurich, Switzerland.
¹⁷ Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹⁸ Faculty of Medicine, University of Tübingen, Tübingen, Germany.
¹⁹ Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany.

PMID: 27575624
DOI: 10.1038/nmeth.3959

Abstract

High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

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OpenMS: a flexible open-source software platform for mass spectrometry data analysis

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OpenMS: a flexible open-source software platform for mass spectrometry data analysis

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