Chemical Sciences: A Manual for CSIR-UGC National Eligibility Test for Lectureship and JRF/OpenMS

OpenMS is an open-source C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL. OpenMS is intended to offer a rich functionality while keeping in mind the design goals of ease-of-use, robustness, extensibility and portability.

OpenMS covers a wide range of functionalities needed to develop software for the analysis of high throughput protein separation and mass spectrometry related data. Among others algorithms for signal processing, feature finding, visualization, map mapping and peptide identification.

OpenMS will be compatible with the upcoming Proteomics Standard Initiative (PSI) formats for MS data.

OpenMS is developed in the groups of Prof. Knut Reinert[1] at the Free University of Berlin and in the group of Prof. Kohlbacher[2] at the University of Tübingen.

Please see the OpenMS website for the most up-to-date information, including download information.

OpenMS has been successfully used for the implementation of The OpenMS Proteomics Pipeline(TOPP). TOPP 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.

References

• 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)