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SimTandem: Similarity Search in Tandem Mass Spectra

  • Jiří Novák
  • Jakub Galgonek
  • David Hoksza
  • Tomáš Skopal
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7404)

Abstract

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 .

Keywords

protein sequences identification tandem mass spectrometry similarity search non-metric access methods SimTandem 

References

  1. 1.
    Dutta, D., Chen, T.: Speeding up Tandem Mass Spectrometry Database Search: Metric Embeddings and Fast Near Neighbor Search. Bioinf. 23(5), 612–618 (2007)CrossRefGoogle Scholar
  2. 2.
    Novák, J., Hoksza, D., Lokoč, J., Skopal, T.: On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds.) ISBRA 2012. LNCS, vol. 7292, pp. 189–200. Springer, Heidelberg (2012)CrossRefGoogle Scholar
  3. 3.
    Novák, J., Skopal, T., Hoksza, D., Lokoč, J.: Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications. Journal of Discrete Algorithms 13, 19–31 (2012)MathSciNetMATHCrossRefGoogle Scholar
  4. 4.
    Ramakrishnan, S.R., et al.: A Fast Coarse Filtering Method for Peptide Identification by Mass Spectrometry. Bioinf. 22(12), 1524–1531 (2006)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Jiří Novák
    • 1
  • Jakub Galgonek
    • 1
  • David Hoksza
    • 1
  • Tomáš Skopal
    • 1
  1. 1.Siret Research Group, Faculty of Mathematics and PhysicsCharles University in PraguePragueCzech Republic

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