Abstract. Mass spectrometry is the work-horse technology of the emerging eld of metabolomics. The identication of mass signals remains the largest bottleneck for a non-targeted approach: due to the analytical method, each metabolite in a complex mixture will give rise to a number of mass signals. In contrast to GC/MS measurements, for soft ionisation methods such as ESI-MS there are no extensive libraries of reference spectra or established deconvolution methods. We present a set of annotation methods which aim to group together mass signals measured from a single metabolite, based on rules for mass dierences and peak shape comparison. Availability: The software and documentation is available as an R package on http://msbi.ipb-halle.de/