SoftwareApplication
identifier: 10.1038/nmeth.3959
name: OpenMS
description: OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.
description: It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D visualization (TOPPView). OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc. It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, Comet, etc. It supports easy integration of OpenMS built tools into workflow engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a 'common tool description' (CTD) scheme. With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development. OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data. The main contributors of OpenMS are currently the Eberhard-Karls-Universität in Tübingen, the Freie Universität Berlin, and the ETH Zürich.
code repository: https://github.com/OpenMS/OpenMS
author: Person
  given name: Ruedi
  family name: Aebersold
  name: Ruedi Aebersold
author: https://orcid.org/0000-0002-2833-6070
author: Person
  given name: Stephan
  family name: Aiche
  name: Stephan Aiche
author: Person
  given name: Chris
  family name: Bielow
  name: Chris Bielow
author: Person
  given name: Hendrik
  family name: Weisser
  name: Hendrik Weisser
author: Person
  given name: Fabian
  family name: Aicheler
  name: Fabian Aicheler
author: Person
  given name: Sandro
  family name: Andreotti
  name: Sandro Andreotti
author: Person
  given name: Hans-Christian
  family name: Ehrlich
  name: Hans-Christian Ehrlich
author: https://orcid.org/0000-0003-4297-6338
author: Person
  given name: Erhan
  family name: Kenar
  name: Erhan Kenar
author: Person
  given name: Xiao
  family name: Liang
  name: Xiao Liang
author: Person
  given name: Sven
  family name: Nahnsen
  name: Sven Nahnsen
author: Person
  given name: Lars
  family name: Nilse
  name: Lars Nilse
author: Person
  given name: Julianus
  family name: Pfeuffer
  name: Julianus Pfeuffer
author: https://orcid.org/0000-0002-1655-6789
author: Person
  given name: Marc
  family name: Rurik
  name: Marc Rurik
author: Person
  given name: Uwe
  family name: Schmitt
  name: Uwe Schmitt
author: Person
  given name: Johannes
  family name: Veit
  name: Johannes Veit
author: Person
  given name: Mathias
  family name: Walzer
  name: Mathias Walzer
author: Person
  given name: David
  family name: Wojnar
  name: David Wojnar
author: Person
  given name: Witold E
  family name: Wolski
  name: Witold E Wolski
author: Person
  given name: Oliver
  family name: Schilling
  name: Oliver Schilling
author: Person
  given name: Jyoti S
  family name: Choudhary
  name: Jyoti S Choudhary
author: Person
  given name: Lars
  family name: Malmström
  name: Lars Malmström
author: Person
  given name: Knut
  family name: Reinert
  name: Knut Reinert
author: https://orcid.org/0000-0003-1739-4598
author: Person
  given name: Hannes L
  family name: Röst
  name: Hannes L Röst
  role name: Principal Investigator
keywords: proteomics
keywords: C++
keywords: mass spectrometry
keywords: metabolomics
programming language: Batchfile
programming language: C
programming language: C++
programming language: CMake
programming language: Cython
programming language: Dockerfile
programming language: HTML
programming language: Linear Programming
programming language: MAXScript
programming language: Mathematical Programming System
programming language: NSIS
programming language: PHP
programming language: Perl
programming language: Python
programming language: R
programming language: Ruby
programming language: Shell
programming language: XSLT
license:
  creative work: creativeWork
    name: BSD-3-Clause

https://orcid.org/0000-0002-2833-6070
type: Person
given name: Timo
family name: Sachsenberg
name: Timo Sachsenberg

https://orcid.org/0000-0003-4297-6338
type: Person
given name: Petra
family name: Gutenbrunner
name: Petra Gutenbrunner

https://orcid.org/0000-0002-1655-6789
type: Person
given name: George
family name: Rosenberger
name: George Rosenberger

https://orcid.org/0000-0003-1739-4598
type: Person
given name: Oliver
family name: Kohlbacher
name: Oliver Kohlbacher