Anal. Chem. In Analytical Chemistry (21 May 2012), doi:10.1021/ac2034216 Multi-stage mass spectrometry (MSn) generating so-called spectral trees has proven itself as a powerful approach in the annotation and structural elucidation of metabolites and is increasingly used in the area of accurate mass LC/MS-based metabolomics. As a consequence, there is a growing need for computational tools specifically designed for the processing and analysis of high mass resolution MSn data. Here we present a novel approach to represent and compare accurate mass fragmentation spectra based on MSn data, enabling metabolite database matching. The approach is based on representing MSn spectra as fingerprints and calculating the degree of similarity between MSn data using the Tanimoto coefficient. The approach was tested using two different spectral libraries, derived from either human or plant metabolites, which currently contain more than 2000 MSn spectra. Both the dereplication and de-novo... - Egon Willighagen