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Proteome Bioinformatics pp 201–211Cite as

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

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 604))

Abstract

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.

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Acknowledgments

The authors wish to thank Andreas Bertsch, Marc Sturm, Clemens Gröpl, and Ole Schulz-Trieglaff for assistance with the figures and critical comments on the manuscript, and the whole OpenMS team for their support.

Author information

Authors and Affiliations

  1. Department Computer Science and Mathematics, Free University of Berlin, Berlin, Germany

    Knut Reinert

  2. Wilhelm Schickard Institute for Computer Science, Tübingen University, Tübingen, Germany

    Oliver Kohlbacher

Authors
  1. Knut Reinert
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  2. Oliver Kohlbacher
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Corresponding author

Correspondence to Oliver Kohlbacher .

Editor information

Editors and Affiliations

  1. Fac. Life Sciences, University of Manchester, Oxford Rd., Manchester, M13 9PT, United Kingdom

    Simon J. Hubbard

  2. Fac. Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, United Kingdom

    Andrew R. Jones

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Reinert, K., Kohlbacher, O. (2010). OpenMS and TOPP: Open Source Software for LC-MS Data Analysis. In: Hubbard, S., Jones, A. (eds) Proteome Bioinformatics. Methods in Molecular Biology™, vol 604. Humana Press. https://doi.org/10.1007/978-1-60761-444-9_14

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  • DOI: https://doi.org/10.1007/978-1-60761-444-9_14

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-443-2

  • Online ISBN: 978-1-60761-444-9

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