title: OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
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.
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.|Department of Genetics, Stanford University, Stanford, California, USA.
authors: Hannes L
authors: HL
authors: Röst
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors: Timo
authors: 0000-0002-2833-6070
authors: T
authors: Sachsenberg
authors: Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
authors: Stephan
authors: S
authors: Aiche
authors: Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.|Metabolomics Core Facility, Berlin Institute of Health, Berlin, Germany.
authors: Chris
authors: C
authors: Bielow
authors: Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK.
authors: Hendrik
authors: H
authors: Weisser
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors: Fabian
authors: F
authors: Aicheler
authors: Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
authors: Sandro
authors: S
authors: Andreotti
authors: Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
authors: Hans-Christian
authors: HC
authors: Ehrlich
authors: Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK.
authors: Petra
authors: 0000-0003-4297-6338
authors: P
authors: Gutenbrunner
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.|Quantitative Biology Center, University of Tübingen, Tübingen, Germany.
authors: Erhan
authors: E
authors: Kenar
authors: International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC), Berlin, Germany.
authors: Xiao
authors: X
authors: Liang
authors: Quantitative Biology Center, University of Tübingen, Tübingen, Germany.
authors: Sven
authors: S
authors: Nahnsen
authors: Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.
authors: Lars
authors: L
authors: Nilse
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors: Julianus
authors: J
authors: Pfeuffer
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors: George
authors: 0000-0002-1655-6789
authors: G
authors: Rosenberger
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors: Marc
authors: M
authors: Rurik
authors: ID Scientific IT Services, ETH Zurich, Zurich, Switzerland.
authors: Uwe
authors: U
authors: Schmitt
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors: Johannes
authors: J
authors: Veit
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.
authors: Mathias
authors: M
authors: Walzer
authors: Quantitative Biology Center, University of Tübingen, Tübingen, Germany.
authors: David
authors: D
authors: Wojnar
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.|Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland.
authors: Witold E
authors: WE
authors: Wolski
authors: Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany.|BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
authors: Oliver
authors: O
authors: Schilling
authors: Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, UK.
authors: Jyoti S
authors: JS
authors: Choudhary
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.|S3IT, University of Zurich, Zurich, Switzerland.
authors: Lars
authors: L
authors: Malmström
authors: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.|Faculty of Science, University of Zurich, Zurich, Switzerland.
authors: Ruedi
authors: R
authors: Aebersold
authors: Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.|Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors: Knut
authors: K
authors: Reinert
authors: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Center for Bioinformatics, University of Tübingen, Tübingen, Germany.|Quantitative Biology Center, University of Tübingen, Tübingen, Germany.|Faculty of Medicine, University of Tübingen, Tübingen, Germany.|Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany.
authors: Oliver
authors: 0000-0003-1739-4598
authors: O
authors: Kohlbacher
mesh_terms: D000375:Aging / Q000097:blood; D001798:Blood Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D001330:Electronic Data Processing; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D058977:Molecular Sequence Annotation; D000071696:Proteogenomics / Q000379:methods; D040901:Proteomics / Q000379:methods*; D012984:Software; D057188:Workflow
chemical_list: D001798:Blood Proteins