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Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W481-4. doi: 10.1093/nar/gkn194. Epub 2008 Apr 28.

MassTRIX: mass translator into pathways.

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Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M├╝nchen, German Research Center for Environmental Health (GmbH), Ingolst├Ądter Landstrasse 1, 85764 Neuherberg, Germany.


Recent technical advances in mass spectrometry (MS) have brought the field of metabolomics to a point where large numbers of metabolites from numerous prokaryotic and eukaryotic organisms can now be easily and precisely detected. The challenge today lies in the correct annotation of these metabolites on the basis of their accurate measured masses. Assignment of bulk chemical formula is generally possible, but without consideration of the biological and genomic context, concrete metabolite annotations remain difficult and uncertain. MassTRIX responds to this challenge by providing a hypothesis-driven approach to high precision MS data annotation. It presents the identified chemical compounds in their genomic context as differentially colored objects on KEGG pathway maps. Information on gene transcription or differences in the gene complement (e.g. samples from different bacterial strains) can be easily added. The user can thus interpret the metabolic state of the organism in the context of its potential and, in the case of submitted transcriptomics data, real enzymatic capacities. The MassTRIX web server is freely accessible at

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