# OpenMS

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> Markdown URL: https://mediated.wiki/source/OpenMS.md
> Source: https://en.wikipedia.org/wiki/OpenMS
> Source revision: 1314977305
> License: Creative Commons Attribution-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/)

{{Infobox software
| name = OpenMS
| title = OpenMS
| logo = 
| logo caption = 
| screenshot = 
| caption = 
| collapsible = 
| author = 
| developer = [https://github.com/OpenMS/OpenMS/blob/develop/AUTHORS Over 65 individuals]
| released = {{Start date and age|2007|07|01|df=yes}}
| latest release version = 3.2.0
| latest release date = {{Start date and age|2024|09|18|df=yes}}
| discontinued = 
| programming language = [C++](/source/C%2B%2B) (with bindings to [Python](/source/Python_(programming_language)))
| operating system = [Linux](/source/Linux), [Windows](/source/Windows), [MacOS](/source/MacOS)
| platform = [x86-64](/source/x86-64), ARM
| size = {{Nowrap|215 MB}}<ref name="OpenMS_releases">[https://github.com/OpenMS/OpenMS/releases OpenMS releases]</ref>
| language = English
| status = 
| genre = [Bioinformatics](/source/Bioinformatics) / [Mass spectrometry software](/source/Mass_spectrometry_software)
| license = [BSD licenses](/source/BSD_licenses) 3-clause
| alexa = 
| website = {{URL|https://openms.de}}
}}

'''OpenMS''' is an open-source project for data analysis and processing in [mass spectrometry](/source/mass_spectrometry) and is released under the [3-clause BSD licence](/source/BSD_licenses). It supports most common operating systems including [Microsoft Windows](/source/Microsoft_Windows), [MacOS](/source/MacOS) and [Linux](/source/Linux).<ref name="openms_pubv2">{{cite journal |vauthors=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 |title=OpenMS: a flexible open-source software platform for mass spectrometry data analysis |journal=Nat. Methods |volume=13 |issue=9 |pages=741–8 |year=2016 |pmid=27575624 |doi=10.1038/nmeth.3959 |s2cid=873670 |url=http://edoc.mdc-berlin.de/15966/13/15966oa.pdf }}</ref>
<ref name="openms_pubv3">{{cite journal |vauthors=Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni PD, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, Boudaud B, Bernt M, Patikas N, Pilz M, Startek MP, Kutuzova S, Heumos L, Charkow J, Sing JC, Feroz A, Siraj A, Weisser H, Dijkstra TM, Perez-Riverol Y, Röst H, Kohlbacher O, Sachsenberg T|title=OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data |journal=Nat. Methods |volume=21 |issue=3 |pages=365–67 |year=2024 |pmid=38366242|doi=10.1038/s41592-024-02197-7}}</ref>

OpenMS has tools for analysis of [proteomics](/source/protein_mass_spectrometry) 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](/source/Label-free_quantification) and isotopic-label based quantification (such as [iTRAQ](/source/iTRAQ) and [TMT](/source/Tandem_mass_tag) and [SILAC](/source/Stable_isotope_labeling_by_amino_acids_in_cell_culture)). OpenMS also supports [metabolomics](/source/metabolomics) workflows and targeted analysis of [DIA/SWATH](/source/data-independent_acquisition) data.<ref name="openms_pubv2"/> Furthermore, OpenMS provides tools for the analysis of [cross linking](/source/Cross-link) 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](/source/Bioinformatics_(journal)) in 2007 and 2008 and has since seen continuous releases.<ref name="Sturm-2008">{{Cite journal 
| last1 = Sturm | first1 = M. 
| last2 = Bertsch | first2 = A. 
| last3 = Gröpl | first3 = C. 
| last4 = Hildebrandt | first4 = A. 
| last5 = Hussong | first5 = R. 
| last6 = Lange | first6 = E. 
| last7 = Pfeifer | first7 = N. 
| last8 = Schulz-Trieglaff | first8 = O. 
| last9 = Zerck | first9 = A. 
| last10 = Reinert | first10 = K. 
| last11 = Kohlbacher | first11 = O. 
| title = OpenMS – an open-source software framework for mass spectrometry 
| doi = 10.1186/1471-2105-9-163 
| journal = BMC Bioinformatics 
| volume = 9 
| page = 163 
| year = 2008 
| pmid = 18366760 
| pmc =2311306 
| doi-access = free 
}}</ref><ref name="Kohlbacher-2007">{{Cite journal 
| last1 = Kohlbacher | first1 = O. 
| last2 = Reinert | first2 = K. 
| last3 = Gropl | first3 = C. 
| last4 = Lange | first4 = E. 
| last5 = Pfeifer | first5 = N. 
| last6 = Schulz-Trieglaff | first6 = O. 
| last7 = Sturm | first7 = M. 
| doi = 10.1093/bioinformatics/btl299 
| title = TOPP--the OpenMS proteomics pipeline 
| journal = Bioinformatics 
| volume = 23 
| issue = 2 
| pages = e191–e197 
| year = 2007 
| pmid = 17237091 
| doi-access =  
}}</ref>
In 2009, the visualization tool TOPPView was published<ref name="Sturm-2009">{{Cite journal 
| last1 = Sturm | first1 = M. 
| last2 = Kohlbacher | first2 = O. 
| doi = 10.1021/pr900171m 
| title = TOPPView: An Open-Source Viewer for Mass Spectrometry Data 
| journal = Journal of Proteome Research 
| volume = 8 
| issue = 7 
| pages = 3760–3763 
| year = 2009 
| pmid = 19425593 
}}</ref> and in 2012, the workflow manager and editor TOPPAS was described.<ref name="Junker-2012">{{Cite journal 
| last1 = Junker | first1 = J. 
| last2 = Bielow | first2 = C. 
| last3 = Bertsch | first3 = A. 
| last4 = Sturm | first4 = M. 
| last5 = Reinert | first5 = K. 
| last6 = Kohlbacher | first6 = O. 
| doi = 10.1021/pr300187f 
| title = TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data 
| journal = Journal of Proteome Research 
| volume = 11 
| issue = 7 
| pages = 3914–3920 
| year = 2012 
| pmid = 22583024 
}}</ref> In 2013, a complete high-throughput [label-free](/source/Label-free_quantification) analysis pipeline using OpenMS 1.8 was described and compared with similar, [proprietary software](/source/proprietary_software) (such as [MaxQuant](/source/MaxQuant) and [Progenesis QI](/source/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 [...]".<ref name="Weisser-2013">{{Cite journal 
| last1 = Weisser | first1 = H. 
| last2 = Nahnsen | first2 = S. 
| last3 = Grossmann | first3 = J. 
| last4 = Nilse | first4 = L. 
| last5 = Quandt | first5 = A. 
| last6 = Brauer | first6 = H. 
| last7 = Sturm | first7 = M. 
| last8 = Kenar | first8 = E. 
| last9 = Kohlbacher | first9 = O. 
| last10 = Aebersold 
| doi = 10.1021/pr300992u | first10 = R. 
| last11 = Malmström | first11 = L. 
| title = An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics 
| journal = Journal of Proteome Research 
| volume = 12 
| issue = 4 
| pages = 1628–44 
| year = 2013 
| pmid = 23391308 
}}</ref>

The OpenMS 1.10 release contained several new analysis tools, including OpenSWATH (a tool for targeted [DIA data analysis](/source/data-independent_acquisition)), a [metabolomics](/source/metabolomics) feature finder and a [TMT](/source/Tandem_mass_tag) analysis tool. Furthermore, full support for TraML 1.0.0 and the search engine MyriMatch were added.<ref>{{Cite web  | title = OpenMS 1.10 released | url = https://open-ms.sourceforge.net/openms-1-10-released/ | access-date = 4 July 2013 }}</ref> The OpenMS 1.11 release was the first release to contain fully integrated bindings to the [Python](/source/Python_(programming_language)) programming language (termed pyOpenMS).<ref name="pypi.python.org">{{Cite web  | title = pyopenms 1.11: Python Package Index | url = https://pypi.python.org/pypi/pyopenms | access-date = 27 October 2013 }}</ref> In addition, new tools were added to support QcML (for quality control) and for [metabolomics](/source/metabolomics) accurate mass analysis. Multiple tools were significantly improved with regard to memory and CPU performance.<ref>{{Cite web  | title = OpenMS 1.11 released | url = https://open-ms.sourceforge.net/openms-1-11-released/ | access-date = 27 October 2013 }}</ref>

With OpenMS 2.0, released in April 2015, the project provides a new version that has been completely cleared of [GPL](/source/GPL) code and uses git (in combination with [GitHub](/source/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.<ref name="pmid25927999">{{cite journal |vauthors=Röst HL, Schmitt U, Aebersold R, Malmström L |title=Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry |journal=PLOS ONE |volume=10 |issue=4 |article-number=e0125108 |year=2015 |pmid=25927999 |pmc=4416046 |doi=10.1371/journal.pone.0125108 |bibcode=2015PLoSO..1025108R |doi-access=free }}</ref> In 2016, the new features of OpenMS 2.0 were described in an article in [Nature Methods](/source/Nature_Methods).<ref name="openms_pubv2"/>

In 2024, OpenMS 3.0<ref name="openms_pubv3"/> was released, providing support for a wide array of data analysis task in proteomics, metabolomics and MS-based transcriptomics.

OpenMS is currently developed with contributions from the group of Knut Reinert<ref>[http://www.inf.fu-berlin.de/inst/ag-bio/ Reinert group]</ref> at the [Free University of Berlin](/source/Free_University_of_Berlin), the group of Oliver Kohlbacher<ref>[http://www-bs.informatik.uni-tuebingen.de/ Kohlbacher group]</ref> at the [University of Tübingen](/source/University_of_T%C3%BCbingen) and the group of [http://roestlab.org/ Hannes Roest]<ref>{{Cite web |last=Roest |first=Hannes |title=Roest group |url=http://roestlab.org/ }}</ref> at [University of Toronto](/source/University_of_Toronto).

== 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](/source/Python_(programming_language)) 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](/source/BSD_licenses) (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](/source/Label-free_quantification) and isotopic-label based quantification (such as [iTRAQ](/source/iTRAQ) and [TMT](/source/Tandem_mass_tag) and [SILAC](/source/Stable_isotope_labeling_by_amino_acids_in_cell_culture)).

The following graphical applications are part an OpenMS release:

* 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](/source/Selected_reaction_monitoring) experiments (in version 1.10). OpenMS is compatible with current and upcoming Proteomics Standard Initiative (PSI) formats for mass spectrometric data.
* TOPPAS is a graphical application to build and execute data processing pipelines which consist of TOPP tools.

== Releases ==

{| class="wikitable sortable"
|-
! Version
! Date
! Features
|-
| {{Version |o |1.6.0 | sortKey="1.6.0"}}
| November 2009
| New version of TOPPAS, reading of compressed XML files, identification-based alignment
|-
| {{Version |o |1.7.0 | sortKey="1.7.0"}}
| September 2010
| Protein quantification, protXML support, create Inclusion/Exclusion lists
|-
| {{Version |o |1.8.0 | sortKey="1.8.0"}}
| March 2011
| Display identification results, QT Clustering-based feature linking
|-
| {{Version |o |1.9.0 | sortKey="1.9.0"}}
| February 2012
| [metabolomics](/source/metabolomics) support, feature detection in raw (profile) data
|-
| {{Version |o |1.10.0 | sortKey="1.10.0"}}
| March 2013
| [KNIME](/source/KNIME) integration, support for targeted SWATH-MS analysis, TraML support, SuperHirn integration, MyriMatch support
|-
| {{Version |o |1.11.0 | sortKey="1.11.0"}}
| August 2013
| Support for [Python](/source/Python_(programming_language)) bindings, performance improvements, Mascot 2.4 support
|-
| {{Version |o |2.0 | sortKey="2.0"}}
| April 2015
| mzQuantL, mzIdentML, mzTab, indexed [mzML](/source/mzML), Removal of [GPL](/source/GPL) code, Switch to [git](/source/git_(software)), Support for Fido, MSGF+, Percolator
|-
| {{Version |o |2.0.1 | sortKey="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
|-
| {{Version |o |2.1.0 | sortKey="2.1.0"}}
| November 2016
| Metabolite SWATH-MS support, lowess-transformations for RT alignment, improved metabolic feature finding
|-
| {{Version |o |2.2.0 | sortKey="2.2.0"}}
| July 2017 
| Fast feature linking using a KD tree, RNA cross-linking support, SpectraST support, scanning SWATH support, [SQLite](/source/SQLite) file formats
|-
| {{Version |o |2.3.0 | sortKey="2.3.0"}}
| January 2018
| Protein-Protein Crosslinking, support for Comet, support for fractions, TMT 11plex, improved build for Python bindings
|-
| {{Version |o |2.4.0 | sortKey="2.4.0"}}
| October 2018
| Support MaraCluster, Crux, MSFragger, MSstats, SIRIUS, visualization of ion mobility and DIA, library improvements
|-
| {{Version |o |2.5.0 | sortKey="2.5.0"}}
| February 2020
| Support RNA mass spectrometry, QualityControl workflow, extended OpenSWATH support, ProteomicsLFQ
|-
| {{Version |o | 2.6.0 | sortKey="2.6.0"}}
| September 2020
| PyOpenMS [wheel](/source/python_wheel) builds, Database suitability tool, SLIM labelling support
|-
| {{Version|o|2.7.0|sortKey="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
|-
| {{Version|o|3.1.0|sortKey="3.1.0"}}
| July 2023
| Added FLASHDeconv, and FLASHDeconvWizard GUI. Removed obsolete tool adapters. Major improvements to documentation.
|-
|{{Version|o|3.1.0|sortKey="3.1.0"}}
|October 2023
|Added SageAdapter; Require some advanced instruction sets (SSE3, AVX, Neon). Documentation fixes (TOPPAS and developer tutorial).
|-
| {{Version|c|3.2.0|sortKey="3.2.0"}}
|September 2024
|Support SubsetNeighborSearch (SNS). SiriusAdapter reworked. Various improvements to TOPPView and TOPPAS. Export for Common Workflow Language (CWL).
|}
<small>{{Version|l|show=11101}}</small>

== See also ==
* [ProteoWizard](/source/ProteoWizard)
* [Trans-Proteomic Pipeline](/source/Trans-Proteomic_Pipeline)
* [Mass spectrometry software](/source/Mass_spectrometry_software)

== References ==
<references />

*

== External links ==
* [https://www.openms.de/ OpenMS Project Homepage]
* {{GitHub|OpenMS/OpenMS}}

Category:Free science software
Category:Bioinformatics software
Category:Mass spectrometry software
Category:Proteomics
Category:Software using the BSD license

---
Adapted from the Wikipedia article [OpenMS](https://en.wikipedia.org/wiki/OpenMS) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/OpenMS?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.