About 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 (TOPP Tools) 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, etc. It supports easy integration of OpenMS built tools into workflow engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPP tools concept and a unified parameter handling via a ‘common tool description’ (CTD) scheme.
Important
As part of the Center for Integrative Bioinformatics (CiBi) in the German Network for Bioinformatics deNBI, OpenMS is currently focusing the development efforts on the integration of OpenMS into KNIME. KNIME is a well-established data analysis framework that supports the generation of workflows for data analysis. Using a Common Tool Description (CTD) file which is writeable by every TOPP tool and a node generator program (Generic KNIME Nodes), all TOPP tools can be made available to run in KNIME.
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 University of Toronto.
Contents#
Introduction
OpenMS Applications and Tools
Run Workflows with OpenMS Tools
Tutorials and Quick Start Guides
Develop with OpenMS
Contribute to OpenMS
- Contributor’s Quick Start Guide
- OpenMS Git Workflow
- Write and Label GitHub Issues
- Adding New Tool to The TOPP suite
- The OpenMS pipeline (TOPP)
- What do I have to do to add a new TOPP tool?
- What do I have to do to add a new UTILS tool?
- I want to implement a new file adapter. What is to be done?
- How to create an icon file for a TOPP tool under Windows?
- Develop your Tool in an external project using OpenMS
- The Common Tool Description (CTD)
- Pull Request Checklist
- Reporting Bugs and Issues
- Advanced
Quick Reference