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J Proteome Res. 2015 Mar 6;14(3):1557-65. doi: 10.1021/pr501246w. Epub 2015 Feb 23.

The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation.

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Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany.


The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation of the acquired data. This includes reliable identification of mass spectra and the meaningful integration of taxonomic and functional meta-information from samples containing hundreds of unknown species. To ease these difficulties, we developed a dedicated software suite, the MetaProteomeAnalyzer, an intuitive open-source tool for metaproteomics data analysis and interpretation, which includes multiple search engines and the feature to decrease data redundancy by grouping protein hits to so-called meta-proteins. We also designed a graph database back-end for the MetaProteomeAnalyzer to allow seamless analysis of results. The functionality of the MetaProteomeAnalyzer is demonstrated using a sample of a microbial community taken from a biogas plant.


bioinformatics; environmental proteomics; mass spectrometry; metaproteomics; microbial communities; software

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