Sep 232015

OpenMS / TOPP / TOPPAS 2.0.0


OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software.

 TOPP (The OpenMS Proteomics Pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. We are currently at well over 40 tools, covering everything from basic signal processing of MS data, to wrapping MS/MS search engines, map alignment, retention time prediction, identification mapping/filtering and much more.

TOPPAS (The TOPP Pipeline Assistant ) is a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction thus reduces to simple drag-and-drop of analysis tools and adding connections in between. As building blocks, you can use all TOPP tools and UTILS shipped with OpenMS. Additionally we provide wrappers for external tools. To add your own external tool, all you need to do is to write a little script.


OpenMS Team



  • Linux/ Windows  / MacOsX
  • C++ Compiler





TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data.
Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.
J Proteome Res. 2012 Jul 6;11(7):3914-20. Epub 2012 May 24.

OpenMS and TOPP: open source software for LC-MS data analysis.
Bertsch A, Gröpl C, Reinert K, Kohlbacher O.
Methods Mol Biol. 2011;696:353-67.


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