Metfusion

MetFusion provides an integrative approach to combine data from different sources in order to improve the identification of compounds from metabolomics experiments via MS and NMR data.


Project maintained by mgerlich Hosted on GitHub Pages — Theme by mattgraham

Welcome to MetFusion. MetFusion is an approach to improve compound identification in metabolomics by combining two different analytical methods. Reliable mass spectra and in silico prediction are combined together to improve the compound identification for unknown spectra. The spectral database providing reference spectra is MassBank (www.massbank.jp/). The in silico fragment generation is performed by MetFrag (msbi.ipb-halle.de/MetFrag/). MetFrag is also hosted at github - see https://github.com/s-wolf/MetFrag.

Chemical similarity between both result lists is used to find similar reference spectra in order to improve the ranking of the correct compound retrieved via the MetFrag candidate list. This is useful as compound databases like PubChem or ChemSpider provide way more compounds than public spectral libraries. Unfortunately, compound databases cannot be queried with spectrum information. MetFusion fixes this and allows to approve the in silico prediction with curated spectra information.

Please ensure that you provide correct values for the settings.properties file. A template file is stored at /WebContent/WEB-INF/settings.properties.template. Remove the .template ending and fill in the requested values.

A console/batch version of MetFusion is runnable via de.ipbhalle.metfusion.main.MetFusionBatchMode. It is recommended that you create a runnable jar with this class as main entry in order to perform batch searches. Running this class without arguments will provide a list of possible parameters. The use of either MassBank record files or MetFusion property files (*.mf) is encouraged as they provide all necessary parameter settings.

A web application of MetFusion is also provided. Checking out this project into Eclipse will create a Dynamic Web Project. Adding this project to a Tomcat 7 or Glassfish 3 server will provide a web interface to MetFusion. Tomcat 7 or Glassfish 3 are required due to the use of ICEfaces 2 AJAX library (www.icefaces.org). ICEfaces provide an Eclipse plugin which provides easy setup of the required libraries.

A runnable out-of-the-box version is available as Java jar archive. This is also tagged as version 2.0 in the code.

For further questions, please contact me at mgerlich(at)ipb-halle(dot)de