SimTandem is a tool for protein or peptide sequences identification from tandem mass spectra. The identification is based on the similarity search in databases of already known or predicted protein sequences. Since the size of sequence databases grows rapidly, metric access methods are employed for database indexes. SimTandem implements a previously proposed method, where the M-tree and the TriGen algorithm were used for fast and approximative (i.e., non-metric) search. The recently introduced parameterized Hausdorff distance, which is suitable as a coarse filter for metric indexes, is utilized. SimTandem supports the search of mass spectra with posttranslational modifications, which are quite common problem when mass spectra are interpreted. SimTandem has been implemented as both the on-line web tool and the stand-alone application. SimTandem is freely available at http://www.simtandem.org or http://www.siret.cz/simtandem.