OpenMS is an open-source project for data analysis and processing in

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is use ...

and is released under the 3-clause BSD licence. It supports most common operating systems including

Microsoft Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

MacOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and lapt ...

and

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

. OpenMS has tools for analysis of

proteomics Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

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 Stable Isotope Labeling by/with Amino acids in Cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitativ ...

). OpenMS also supports

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...

workflows and targeted analysis of DIA/SWATH data. Furthermore, OpenMS provides tools for the analysis of

cross linking In chemistry and biology a cross-link is a bond or a short sequence of bonds that links one polymer chain to another. These links may take the form of covalent bonds or ionic bonds and the polymers can be either synthetic polymers or natural ...

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 Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

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 2013, a complete high-throughput label-free analysis pipeline using OpenMS 1.8 was described and compared with similar,

proprietary software Proprietary software is software that is deemed within the free and open-source software to be non-free because its creator, publisher, or other rightsholder or rightsholder partner exercises a legal monopoly afforded by modern copyright and int ...

(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 ... The OpenMS 1.10 release contained several new analysis tools, including OpenSWATH (a tool for targeted DIA data analysis), a

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 Python may refer to: Snakes * Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia ** ''Python'' (genus), a genus of Pythonidae found in Africa and Asia * Python (mythology), a mythical serpent Computing * Python (pro ...

programming language (termed pyOpenMS). In addition, new tools were added to support QcML (for quality control) and for

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 The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general u ...

code and uses git (in combination with

GitHub GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous ...

) 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. In 2016, the new features of OpenMS 2.0 were described in an article in

Nature Methods ''Nature Methods'' is a monthly peer-reviewed scientific journal covering new scientific techniques. It was established in 2004 and is published by Springer Nature under the Nature Portfolio. Like other ''Nature'' journals, there is no external edi ...

. OpenMS is currently developed with contributions from the group of Knut Reinert at the

Free University of Berlin The Free University of Berlin (, often abbreviated as FU Berlin or simply FU) is a public research university in Berlin, Germany. It is consistently ranked among Germany's best universities, with particular strengths in political science and t ...

, the group of Oliver Kohlbacher at the

University of Tübingen The University of Tübingen, officially the Eberhard Karl University of Tübingen (german: Eberhard Karls Universität Tübingen; la, Universitas Eberhardina Carolina), is a public research university located in the city of Tübingen, Baden-Wü ...

and the group of

Ruedi Aebersold Rudolf Aebersold (better known as Ruedi Aebersold born September 12, 1954 ) is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samp ...

ETH Zurich (colloquially) , former_name = eidgenössische polytechnische Schule , image = ETHZ.JPG , image_size = , established = , type = Public , budget = CHF 1.896 billion (2021) , rector = Günther Dissertori , president = Joël Mesot , ac ...

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

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

). 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

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References

External links

OpenMS Project Homepage

OpenMS GitHub Page

PyOpenMS page on PyPI

PyOpenMS tutorial on readthedocs
Free science software Bioinformatics software Mass spectrometry software Proteomics Software using the BSD license

History

Features

Releases

See also

References

External links