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Oliver Kohlbacher and Knut Reinert (2009)

OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

In: Proteome Bioinformatics, ed. by Simon J. Hubbard and Andrew R. Jones, vol. 604, chap. 14, pp. 201-11, Humana Press. Methods in Molecular Biology.

The automatic analysis of mass spectrometry data is becoming more and more important since increasingly larger datasets are readily available that cannot be evaluated manually. This has triggered the development of several open-source software libraries for the automatic analysis of such data. Among those is OpenMS together with TOPP (The OpenMS Proteomics Pipeline). OpenMS is a C++ library for rapid prototyping of complex algorithms for the analysis of mass spectrometry data. Based on the OpenMS library, TOPP provides a collection of tools for the most important tasks in proteomics analysis. The tight coupling of OpenMS and TOPP makes it easy to extend TOPP by adding new tools to the OpenMS library. We describe the overall concepts behind the software and illustrate its use with several examples.