Use MetFrag directly from your browser which makes it pretty easy for beginners
The new MetFrag commandline tool providing additional scoring terms for scoring candidates with MS/MS spectra
Users familiar with R can download MetFrag as R-package
Tools to convert between MetFrag related file formats
MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.
MetFrag can be easily used via the web tool. For high-troughput data processing the commandline version should be most convenient as well as the R-package for users versed in the R programming language.
Version 2010:In silico fragmentation for computer assisted identification of metabolite mass spectra: S Wolf, S Schmidt, M Müller-Hannemann, S Neumann BMC bioinformatics 11 (1), 148 These are the papers in PubMed and google scholar that have cited MetFrag (version 2010) so far.
MetFrag software is published under the terms of the GNU Lesser General Public License version 2.1 or later.