OpenMS
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.
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 Comet, etc.
It supports easy integration of OpenMS built tools into workflow
engines like nextflow, Galaxy, 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.
Table of Contents
Features
- Core C++ library under three-clause BSD licence using modern C++23
- Python bindings to the C++ API through pyOpenMS
- Major community file formats supported (mzML, mzXML, mzIdentXML, pepXML, mzTab, etc.)
- Over 150+ individual analysis tools (TOPP Tools), covering most MS and LC-MS data processing and mining tasks
- Powerful 1D, 2D and 3D visualization tools (TOPPView)
- Support for most MS identification and quantification workflows (targeted, DIA, label-free, isobaric and stable isotope labelled)
- Support for all major platforms (Windows [10, 11], macOS and Linux)
Documentation
Users and developers should start by reading the OpenMS documentation on ReadTheDocs (RTD).
The OpenMS API reference and advanced developer doxygen documentation can be browsed here.
The OpenMS RTD documentation aims at being an entry point for users and developers alike. It is trying to be mostly version-independent and therefore
only consists of one main branch. We may introduce tags for older releases in the future.
The OpenMS API reference has several endpoints:
nightly: OpenMS API reference and advanced developer documentation of nightly releases.release/latest : OpenMS API reference and advanced developer documentation of latest stable release.release/${version} : OpenMS API reference and advanced developer documentation of a specific release, from 3.6.0 on. Older releases are on abibuilder.
Documentation for the Python bindings pyOpenMS can be found on the pyOpenMS online documentation.
Building OpenMS
For developers who want to build OpenMS from source:
The CMake presets build the third-party libraries with vcpkg, as CI does: clone with
--recurse-submodules (or run git submodule update --init vcpkg) and configure with a preset, e.g.
cmake --preset linux-x64-release (cmake --list-presets lists them). Without a preset, OpenMS takes its
dependencies from system packages and CMAKE_PREFIX_PATH (OPENMS_USE_VCPKG=OFF, the default).
For more detailed instructions, see the Developer Tutorial.
Citation
Please cite:
Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data, Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7
The file AUTHORS contains a list of all authors who worked on OpenMS.
