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.^[3]

OpenMS has tools for many common data analysis pipelines used in proteomics, providing algorithms for signal processing, feature finding (including de-isotoping), visualization in 1D (spectra or chromatogram level), 2D and 3D, map mapping and peptide identification. It supports label-free and isotopic-label based quantification (such as iTRAQ and TMT and SILAC). Furthermore, it also supports metabolomics workflows and targeted analysis of DIA/SWATH data.^[3]

To achieve a wide variety of tasks in proteomics, OpenMS provides the The OpenMS Proteomics Pipeline(TOPP) 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.^[3]

History

OpenMS was originally released in 2007 in version 1.0 and was described in two articles published in Bioinformatics in 2007 and 2008.^[4][5] As of 2016, multiple further versions have been released (the latest being 2.0.1 in April 2016).^[2] In 2009, the visualization tool TOPPView was published^[6] and in 2012, the workflow manager and editor TOPPAS was described in a scientific article.^[7] 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 [...]".^[8] In 2015, version 2.0 was released.

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.^[9]

The OpenMS 1.11 release was the first release to contain fully integrated bindings to the Python programming language (termed pyOpenMS).^[10] 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.^[11]

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.^[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] the 4th meeting took place in September 2011 in Berlin,^[14] the 5th OpenMS user meeting took place in Salzburg on October 8 and 9 2012.^[15] The 6th OpenMS user meeting took place in Zurich on September 3 to 5 2013,^[16] the 7th meeting took place from September 3–5, 2014 at the Max Planck-Institute for Molecular Genetics in Berlin.^[17] The 8th user meeting took place September 16 to 18 at the Medizinisches Proteom-Center in Bochum.^[18]

OpenMS is currently developed in the groups of Knut Reinert^[19] at the Free University of Berlin, in the group of Oliver Kohlbacher^[20] at the University of Tübingen and in the group of Ruedi Aebersold^[21] 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 (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.^[7]

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

Releases

See also

• ProteoWizard
• Trans-Proteomic Pipeline
• Mass spectrometry software

References

1. ↑ OpenMS 2.0.1 released
2. 1 2 OpenMS releases
3. 1 2 3 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". Nat. Methods. 13 (9): 741–8. doi:10.1038/nmeth.3959. PMID 27575624. 
4. ↑ Sturm, M.; Bertsch, A.; Gröpl, C.; Hildebrandt, A.; Hussong, R.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Zerck, A.; Reinert, K.; Kohlbacher, O. (2008). "OpenMS – an open-source software framework for mass spectrometry". BMC Bioinformatics. 9: 163. doi:10.1186/1471-2105-9-163. PMC 2311306. PMID 18366760. 
5. ↑ Kohlbacher, O.; Reinert, K.; Gropl, C.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Sturm, M. (2007). "TOPP--the OpenMS proteomics pipeline". Bioinformatics. 23 (2): e191–e197. doi:10.1093/bioinformatics/btl299. PMID 17237091. 
6. ↑ Sturm, M.; Kohlbacher, O. (2009). "TOPPView: An Open-Source Viewer for Mass Spectrometry Data". Journal of Proteome Research. 8 (7): 3760–3763. doi:10.1021/pr900171m. PMID 19425593. 
7. 1 2 Junker, J.; Bielow, C.; Bertsch, A.; Sturm, M.; Reinert, K.; Kohlbacher, O. (2012). "TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data". Journal of Proteome Research. 11 (7): 3914–3920. doi:10.1021/pr300187f. PMID 22583024. 
8. ↑ Weisser, H.; Nahnsen, S.; Grossmann, J.; Nilse, L.; Quandt, A.; Brauer, H.; Sturm, M.; Kenar, E.; Kohlbacher, O.; Aebersold, R.; Malmström, L. (2013). "An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics". Journal of Proteome Research. 12 (4): 1628–44. doi:10.1021/pr300992u. PMID 23391308. 
9. ↑ "OpenMS 1.10 released". Retrieved 4 July 2013. 
10. ↑ "pyopenms 1.11 : Python Package Index". Retrieved 27 October 2013. 
11. ↑ "OpenMS 1.11 released". Retrieved 27 October 2013. 
12. ↑ Röst HL, Schmitt U, Aebersold R, Malmström L (2015). "Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry". PLoS ONE. 10 (4): e0125108. doi:10.1371/journal.pone.0125108. PMC 4416046. PMID 25927999. 
13. ↑ "OpenMS user meeting on the 1-2nd of March 2010". Retrieved 27 October 2013. 
14. ↑ "Fall User Meeting 2011". Retrieved 27 October 2013. 
15. ↑ "5th OpenMS User Meeting – High-performance software for high-throughput proteomics and metabolomics". Retrieved 4 July 2013. 
16. ↑ "6th OpenMS User Meeting – High-performance software for high-throughput proteomics and metabolomics". Retrieved 27 October 2013. 
17. ↑ "7th OpenMS User Meeting – High-performance software for high-throughput proteomics and metabolomics | OpenMS". 
18. ↑ "8th OpenMS User Meeting – High-performance software for high-throughput proteomics and metabolomics | OpenMS". Retrieved 2016-03-30. 
19. ↑ Reinert group
20. ↑ Kohlbacher group
21. ↑ Aebersold group

• 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". Nat. Methods. 13 (9): 741–8. doi:10.1038/nmeth.3959. PMID 27575624. 

External links

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