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OpenMS - an open-source software framework for mass spectrometry.

Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O - BMC Bioinformatics (2008)

Bottom Line: Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow.OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis.This has already been demonstrated in several studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics, Eberhard Karls University Tübingen, Sand 14, 72076 Tübingen, Germany. sturm@informatik.uni-tuebingen.de

ABSTRACT

Background: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow.

Results: We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies.

Conclusion: OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de.

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Related in: MedlinePlus

The data reduction concept of OpenMS. A raw map (top) which is first reduced to a peak map (middle) and finally to a feature map (bottom). The direct reduction of raw to feature map is also possible.
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Figure 2: The data reduction concept of OpenMS. A raw map (top) which is first reduced to a peak map (middle) and finally to a feature map (bottom). The direct reduction of raw to feature map is also possible.

Mentions: Data reduction is a central concept of OpenMS and will now be considered in more detail. Data reduction comprises two transformation steps as displayed in Fig. 2: The conversion of raw spectra (also called continuous spectra or profile spectra) to peak spectra (also called stick spectra) and the conversion of a raw or peak map (a collection of MS spectra produced by an experiment) to a feature map. By feature we denote the two-dimensional signal created by some chemical entity, e.g. a peptide or metabolite. A feature is characterized by its isotopic pattern in mass-to-charge dimension and by the elution profile in retention time dimension.


OpenMS - an open-source software framework for mass spectrometry.

Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O - BMC Bioinformatics (2008)

The data reduction concept of OpenMS. A raw map (top) which is first reduced to a peak map (middle) and finally to a feature map (bottom). The direct reduction of raw to feature map is also possible.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2311306&req=5

Figure 2: The data reduction concept of OpenMS. A raw map (top) which is first reduced to a peak map (middle) and finally to a feature map (bottom). The direct reduction of raw to feature map is also possible.
Mentions: Data reduction is a central concept of OpenMS and will now be considered in more detail. Data reduction comprises two transformation steps as displayed in Fig. 2: The conversion of raw spectra (also called continuous spectra or profile spectra) to peak spectra (also called stick spectra) and the conversion of a raw or peak map (a collection of MS spectra produced by an experiment) to a feature map. By feature we denote the two-dimensional signal created by some chemical entity, e.g. a peptide or metabolite. A feature is characterized by its isotopic pattern in mass-to-charge dimension and by the elution profile in retention time dimension.

Bottom Line: Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow.OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis.This has already been demonstrated in several studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Bioinformatics, Eberhard Karls University Tübingen, Sand 14, 72076 Tübingen, Germany. sturm@informatik.uni-tuebingen.de

ABSTRACT

Background: Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever increasing amounts of data. Consequently, analysis of the data is currently often the bottleneck for experimental studies. Although software tools for many data analysis tasks are available today, they are often hard to combine with each other or not flexible enough to allow for rapid prototyping of a new analysis workflow.

Results: We present OpenMS, a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis. This has already been demonstrated in several studies.

Conclusion: OpenMS is available under the Lesser GNU Public License (LGPL) from the project website at http://www.openms.de.

Show MeSH
Related in: MedlinePlus