OpenMS


OpenMS is an open-source project for data analysis and processing in protein mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, OS X and Linux.
OpenMS has tools for many common data analysis pipelines used in proteomics, providing algorithms for signal processing, feature finding, visualization in 1D, 2D and 3D, map mapping and peptide identification. It supports label-free and isotopic-label based quantification. Furthermore, it also supports metabolomics workflows and targeted analysis of DIA/SWATH data.
To achieve a wide variety of tasks in proteomics, OpenMS provides The OpenMS Proteomics Pipeline which is a set of computational tools that can be chained together to tailor problem-specific analysis pipelines for HPLC-MS data. It transforms most of the OpenMS functionality into small command line tools that are the building blocks for more complex analysis pipelines.

History

OpenMS was originally released in 2007 in version 1.0 and was described in two articles published in Bioinformatics in 2007 and 2008 and has since seen continuous releases.
In 2009, the visualization tool TOPPView was published and in 2012, the workflow manager and editor TOPPAS was described in a scientific article. In 2013, a complete high-throughput label-free analysis pipeline using OpenMS 1.8 was described in the literature and compared with similar, proprietary software. The authors conclude that " all three software solutions produce adequate and largely comparable quantification results; all have some weaknesses, and none can outperform the other two in every aspect that we examined. However, the performance of OpenMS is on par with that of its two tested competitors ".
The OpenMS 1.10 release contained several new analysis tools, including OpenSWATH, a metabolomics feature finder and a TMT analysis tool. Furthermore, full support for TraML 1.0.0 and the search engine MyriMatch were added. The OpenMS 1.11 release was the first release to contain fully integrated bindings to the Python programming language. In addition, several new tools were added such as tools relating to QcML and for metabolomics accurate mass analysis. Multiple tools were significantly improved with regard to memory and CPU performance.
With OpenMS 2.0, released in April 2015, the project provides a new version that has been completely cleared of GPL code and uses git for its version control and ticketing system. Other changes include support for mzIdentML, mzQuantML and mzTab while multiple improvements in the kernel allowed for faster access to data stored in mzML and provided a novel API for accessing mass spectrometric data. In 2016, the new features of OpenMS 2.0 were described in an article in Nature Methods.
Since the inception of the project, a yearly OpenMS user meeting has been held at several universities where developers and users of the framework had the chance to present new features of OpenMS and direct, biological applications of OpenMS. The 3rd OpenMS user meeting took place in March 2010 in Dortmund, with the next meetings taking place in Berlin, Salzburg, Zurich, Berlin, Bochum and Tübingen.
OpenMS is currently developed in the groups of Knut Reinert at the Free University of Berlin, in the group of Oliver Kohlbacher at the University of Tübingen and in the group of Ruedi Aebersold at ETH Zurich.

Features

OpenMS provides several features to users and developers, foremost providing a set of over 100 different executable tools than can be chained together into pipelines for proteomics data analysis. It also provides visualization tools for spectra and chromatograms, mass spectrometric heat maps as well as a three-dimensional visualization of a mass spectrometry experiment. Finally, OpenMS also provides a C++ library for LC/MS data management and analyses accessible to developers to create new tools and implement their own algorithms using the OpenMS library. OpenMS is free software available under the 3-clause BSD licence.
Among others, it provides algorithms for signal processing, feature finding, visualization, map mapping and peptide identification. It supports label-free and isotopic-label based quantification.
TOPPView is a viewer software that allows visualization of mass spectrometric data on MS1 and MS2 level as well as in 3D; additionally it also displays chromatographic data from SRM experiments. TOPPAS is a graphic integrated workflow manager that allows chaining the TOPP tools into a reusable and reproducible workflow.
OpenMS is compatible with the current and the upcoming Proteomics Standard Initiative formats for mass spectrometric data.

Releases

VersionDateFeatures
November 2009New version of TOPPAS, reading of compressed XML files, identification-based alignment
September 2010Protein quantification, protXML support, create Inclusion/Exclusion lists
March 2011Display identification results, QT Clustering-based feature linking
February 2012metabolomics support, feature detection in raw data
March 2013KNIME integration, support for targeted SWATH-MS analysis, TraML support, SuperHirn integration, MyriMatch support
August 2013Support for Python bindings, performance improvements, Mascot 2.4 support
April 2015mzQuantL, mzIdentML, mzTab, indexed mzML, Removal of GPL code, Switch to git, Support for Fido, MSGF+, Percolator
April 2016faster file reading, improved support for mzIdentML and mzTab, elemental flux analysis, targeted assay generation, Support for Comet and Luciphor
November 2016Metabolite SWATH-MS support, lowess-transformations for RT alignment, improved metabolic feature finding
July 2017Fast feature linking using a KD tree, RNA cross-linking support, SpectraST support, scanning SWATH support, SQLite file formats
January 2018Protein-Protein Crosslinking, support for Comet, support for fractions, TMT 11plex, improved build for Python bindings
October 2018Support MaraCluster, Crux, MSFragger, MSstats, SIRIUS, visualization of ion mobility and DIA, library improvements