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Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry

  • Conference paper
Research in Computational Molecular Biology (RECOMB 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

Filtration techniques, in the form of rapid elimination of candidate sequences while retaining the true one, are key ingredients of database searches in genomics. Although SEQUEST and Mascot are sometimes referred to as “BLAST for mass-spectrometry”, the key algorithmic idea of BLAST (filtration) was never implemented in these tools. As a result MS/MS protein identification tools are becoming too time-consuming for many applications including search for post-translationally modified peptides. Moreover, matching millions of spectra against all known proteins will soon make these tools too slow in the same way that “genome vs. genome” comparisons instantly made BLAST too slow. We describe the development of filters for MS/MS database searches that dramatically reduce the running time and effectively remove the bottlenecks in searching the huge space of protein modifications. Our approach, based on a probability model for determining the accuracy of sequence tags, achieves superior results compared to GutenTag, a popular tag generation algorithm.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0114, USA

    Ari Frank & Pavel Pevzner

  2. Department of Bioinformatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0419, USA

    Stephen Tanner

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  1. Ari Frank
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  2. Stephen Tanner
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  3. Pavel Pevzner
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Frank, A., Tanner, S., Pevzner, P. (2005). Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_25

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  • DOI: https://doi.org/10.1007/11415770_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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