An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline


OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.

It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) and powerful 2D and 3D visualization(TOPPView).


OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH, ….

It provides  built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like XTandem,  Mascot, OMSSA, etc.

It supports easy integration of OpenMS built tools into workflow engines like KnimeGalaxyWS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling (CTD).


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 Zurich.