Non-metric similarity search of tandem mass spectra including posttranslational modifications
Journal of Discrete Algorithms
On optimizing the non-metric similarity search in tandem mass spectra by clustering
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
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SimTandem is a tool for fast identification of protein and peptide sequences from tandem mass spectra. The identification is based on similarity search of spectra captured by a tandem mass spectrometer in databases of theoretical mass spectra generated from databases of known protein sequences. Since the number of protein sequences in the databases grows rapidly and a sequential scan over the entire database of spectra is time-consuming, the non-metric access methods are employed as the database indexing techniques. SimTandem is based on a previously proposed method and is freely available at http://www.simtandem.org or http://www.siret.cz/simtandem.