On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering

  • Jiří Novák
  • David Hoksza
  • Jakub Lokoč
  • Tomáš Skopal
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7292)


Tandem mass spectrometry is a well-known technique for identification of protein sequences from an ”in vitro” sample. To identify the sequences from spectra captured by a spectrometer, the similarity search in a database of hypothetical mass spectra is often used. For this purpose, a database of known protein sequences is utilized to generate the hypothetical spectra. Since the number of sequences in the databases grows rapidly over the time, several approaches have been proposed to index the databases of mass spectra. In this paper, we improve an approach based on the non-metric similarity search where the M-tree and the TriGen algorithm are employed for fast and approximative search. We show that preprocessing of mass spectra by clustering speeds up the identification of sequences more than 100× with respect to the sequential scan of the entire database. Moreover, when the protein candidates are refined by sequential scan in the postprocessing step, the whole approach exhibits precision similar to that of sequential scan over the entire database (over 90%).


Tandem mass spectrometry similarity search non-metric access methods protein sequences identification spectral clustering 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

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

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