OpenMS

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.[3][4] In 2009, the visualization tool TOPPView was published[5] and in 2012, the workflow manager and editor TOPPAS was described in a scientific article.[6] 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 (such as MaxQuant and Progenesis). 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 [...]".[7]

The OpenMS 1.10 release contained several new analysis tools, including OpenSWATH (a tool for targeted DIA data analysis), a metabolomics feature finder and a TMT analysis tool. Furthermore, full support for TraML 1.0.0 and the search engine MyriMatch were added.[8] The OpenMS 1.11 release was the first release to contain fully integrated bindings to the Python programming language (termed pyOpenMS).[9] In addition, several new tools were added such as tools relating to QcML (for quality control) and for metabolomics accurate mass analysis. Multiple tools were significantly improved with regard to memory and CPU performance.[10]

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 (in combination with GitHub) 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.[11] In 2016, the new features of OpenMS 2.0 were described in an article in Nature Methods.[12]

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,[13] with the next meetings taking place in Berlin (4th meeting in September 2011),[14] Salzburg (5th meeting in October 2012),[15] Zurich (6th meeting in September 2013),[16] Berlin (7th meeting in September 2014),[17] Bochum (8th user meeting in September 2015)[18] and Tübingen (9th meeting in September 2016).[19]

OpenMS is currently developed in the groups of Knut Reinert[20] at the Free University of Berlin, in the group of Oliver Kohlbacher[21] at the University of Tübingen and in the group of Ruedi Aebersold[22] at ETH Zurich.

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 (the TOPP Tools). It also provides visualization tools for spectra and chromatograms (1D), mass spectrometric heat maps (2D m/z vs RT) as well as a three-dimensional visualization of a mass spectrometry experiment. Finally, OpenMS also provides a C++ library (with bindings to Python available since 1.11) 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 (previously under the LGPL).

Among others, it provides algorithms for signal processing, feature finding (including de-isotoping), visualization, map mapping and peptide identification. It supports label-free and isotopic-label based quantification (such as iTRAQ and TMT and SILAC).

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 (in version 1.10). TOPPAS is a graphic integrated workflow manager that allows chaining the TOPP tools into a reusable and reproducible workflow.[6]

OpenMS is compatible with the current and the upcoming Proteomics Standard Initiative (PSI) formats for mass spectrometric data.

• ProteoWizard
• Trans-Proteomic Pipeline
• Mass spectrometry software

• Sturm M, Bertsch A, Groepl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O: OpenMS – An open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9:163.(fulltext)
• Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M: TOPP - the OpenMS proteomics pipeline. Bioinformatics 2007, 23(2):e191-7. (fulltext)
• Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O (2016). "OpenMS: a flexible open-source software platform for mass spectrometry data analysis" (PDF). Nat. Methods. 13 (9): 741–8. doi:10.1038/nmeth.3959. PMID 27575624. S2CID 873670.

• OpenMS Project Homepage
• OpenMS GitHub Page
• OpenMS Documentation
• OpenMS Sourceforge Page (only code before 2014)
• PyOpenMS page on PyPI