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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. 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 DIA/SWATH targeted analysis. 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. == History == OpenMS was originally released in 2007 in version 1.0 and was described in two articles published in Bioinformatics in 2007 and 2008. As of 2015, multiple further versions have been released (the latest being 2.0 in April 2015).〔(OpenMS releases )〕 In 2009, the visualization tool TOPPView was published and in 2012, the workflow manager and editor TOPPAS was described in a scientific article. 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 ()". 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. The OpenMS 1.11 release was the first release to contain fully integrated bindings to the Python programming language (termed pyOpenMS). 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. 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. 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, the 4th meeting took place in September 2011 in Berlin, the 5th OpenMS user meeting took place in Salzburg on October 8 and 9 2012. The 6th OpenMS user meeting took place in Zurich on September 3 to 5 2013, the 7th meeting took place from September 3–5, 2014 at the Max Planck-Institute for Molecular Genetics in Berlin. OpenMS is currently developed in the groups of Knut Reinert〔(Reinert group )〕 at the Free University of Berlin, in the group of Oliver Kohlbacher〔(Kohlbacher group )〕 at the University of Tübingen and in the group of Ruedi Aebersold〔(Aebersold group )〕 at ETH Zurich. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「OpenMS」の詳細全文を読む スポンサード リンク
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