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PLoS One. 2012;7(6):e40096. doi: 10.1371/journal.pone.0040096. Epub 2012 Jun 29.

MetaboSearch: tool for mass-based metabolite identification using multiple databases.

Author information

1
Department of Oncology, Georgetown University, Washington, DC, United States of America.

Abstract

Searching metabolites against databases according to their masses is often the first step in metabolite identification for a mass spectrometry-based untargeted metabolomics study. Major metabolite databases include Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LIPID MAPS. Since each one of these databases covers only a fraction of the metabolome, integration of the search results from these databases is expected to yield a more comprehensive coverage. However, the manual combination of multiple search results is generally difficult when identification of hundreds of metabolites is desired. We have implemented a web-based software tool that enables simultaneous mass-based search against the four major databases, and the integration of the results. In addition, more complete chemical identifier information for the metabolites is retrieved by cross-referencing multiple databases. The search results are merged based on IUPAC International Chemical Identifier (InChI) keys. Besides a simple list of m/z values, the software can accept the ion annotation information as input for enhanced metabolite identification. The performance of the software is demonstrated on mass spectrometry data acquired in both positive and negative ionization modes. Compared with search results from individual databases, MetaboSearch provides better coverage of the metabolome and more complete chemical identifier information.

AVAILABILITY:

The software tool is available at http://omics.georgetown.edu/MetaboSearch.html.

PMID:
22768229
PMCID:
PMC3387018
DOI:
10.1371/journal.pone.0040096
[Indexed for MEDLINE]
Free PMC Article
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