OpenMS
Developer(s) | Over 65 individuals |
---|---|
Initial release | 1 July 2007; 17 years ago (2007-07-01) |
Stable release | 3.1.0 / 25 October 2023; 10 months ago (2023-10-25) |
Repository |
|
Written in | C++ (with bindings to Python) |
Operating system | Linux, Windows, MacOS |
Size | 215 MB[1] |
Available in | English |
Type | Bioinformatics / Mass spectrometry software |
License | BSD licenses 3-clause |
Website | openms |
OpenMS is an open-source project for data analysis and processing in mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, MacOS and Linux.[2]
OpenMS has tools for analysis of proteomics data, 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). OpenMS also supports metabolomics workflows and targeted analysis of DIA/SWATH data.[2] Furthermore, OpenMS provides tools for the analysis of cross linking data, including protein-protein, protein-RNA and protein-DNA cross linking. Lastly, OpenMS provides tools for analysis of RNA mass spectrometry data.
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.[3][4] In 2009, the visualization tool TOPPView was published[5] and in 2012, the workflow manager and editor TOPPAS was described.[6] In 2013, a complete high-throughput label-free analysis pipeline using OpenMS 1.8 was described and compared with similar, proprietary software (such as MaxQuant and Progenesis QI). 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, new tools were added to support 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 improvements in the kernel allow for faster access to data stored in mzML and provide 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.[2]
OpenMS is currently developed with contributions from the group of Knut Reinert[12] at the Free University of Berlin, the group of Oliver Kohlbacher[13] at the University of Tübingen and the group of Ruedi Aebersold[14] at ETH Zurich.
Features
OpenMS provides a set of over 100 different executable tools than can be chained together into pipelines for mass spectrometry 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 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). OpenMS is compatible with current and upcoming Proteomics Standard Initiative (PSI) formats for mass spectrometric data.
Releases
Version | Date | Features | |
---|---|---|---|
Old version, no longer maintained: 1.6.0 | November 2009 | New version of TOPPAS, reading of compressed XML files, identification-based alignment | |
Old version, no longer maintained: 1.7.0 | September 2010 | Protein quantification, protXML support, create Inclusion/Exclusion lists | |
Old version, no longer maintained: 1.8.0 | March 2011 | Display identification results, QT Clustering-based feature linking | |
Old version, no longer maintained: 1.9.0 | February 2012 | metabolomics support, feature detection in raw (profile) data | |
Old version, no longer maintained: 1.10.0 | March 2013 | KNIME integration, support for targeted SWATH-MS analysis, TraML support, SuperHirn integration, MyriMatch support | |
Old version, no longer maintained: 1.11.0 | August 2013 | Support for Python bindings, performance improvements, Mascot 2.4 support | |
Old version, no longer maintained: 2.0 | April 2015 | mzQuantL, mzIdentML, mzTab, indexed mzML, Removal of GPL code, Switch to git, Support for Fido, MSGF+, Percolator | |
Old version, no longer maintained: 2.0.1 | April 2016 | faster file reading, improved support for mzIdentML and mzTab, elemental flux analysis, targeted assay generation, Support for Comet and Luciphor | |
Old version, no longer maintained: 2.1.0 | November 2016 | Metabolite SWATH-MS support, lowess-transformations for RT alignment, improved metabolic feature finding | |
Old version, no longer maintained: 2.2.0 | July 2017 | Fast feature linking using a KD tree, RNA cross-linking support, SpectraST support, scanning SWATH support, SQLite file formats | |
Old version, no longer maintained: 2.3.0 | January 2018 | Protein-Protein Crosslinking, support for Comet, support for fractions, TMT 11plex, improved build for Python bindings | |
Old version, no longer maintained: 2.4.0 | October 2018 | Support MaraCluster, Crux, MSFragger, MSstats, SIRIUS, visualization of ion mobility and DIA, library improvements | |
Old version, no longer maintained: 2.5.0 | February 2020 | Support RNA mass spectrometry, QualityControl workflow, extended OpenSWATH support, ProteomicsLFQ | |
Old version, no longer maintained: 2.6.0 | September 2020 | PyOpenMS wheel builds, Database suitability tool, SLIM labelling support | |
Old version, no longer maintained: 2.7.0 | July 2021 | Improved support of NOVOR and MSFragger and for SIRIUS 4.9.0, export of mzQC format in QCCalculator, improved reading and writing of NIST MSP files | |
Current stable version: 3.0.0 | July 2023 | Added FLASHDeconv, and FLASHDeconvWizard GUI. Removed obsolete tool adapters. Major improvements to documentation. |
See also
References
- ^ OpenMS releases
- ^ a b c 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ "OpenMS 1.10 released". Retrieved 4 July 2013.
- ^ "pyopenms 1.11 : Python Package Index". Retrieved 27 October 2013.
- ^ "OpenMS 1.11 released". Retrieved 27 October 2013.
- ^ 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. Bibcode:2015PLoSO..1025108R. doi:10.1371/journal.pone.0125108. PMC 4416046. PMID 25927999.
- ^ Reinert group
- ^ Kohlbacher group
- ^ "Aebersold group". Archived from the original on 2011-07-20. Retrieved 2013-07-01.
External links
- OpenMS Project Homepage
- OpenMS on GitHub