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Constrained De Novo Sequencing of Peptides with Application to Conotoxins

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Research in Computational Molecular Biology (RECOMB 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6577))

Abstract

We describe algorithms for incorporating prior sequence knowledge into the candidate generation stage of de novo peptide sequencing by tandem mass spectrometry. We focus on two types of prior knowledge: homology to known sequences encoded by a regular expression or position-specific score matrix, and amino acid content encoded by a multiset of required residues. We show an application to de novo sequencing of cone snail toxins, which are molecules of special interest as pharmaceutical leads and as probes to study ion channels. Cone snail toxins usually contain 2, 4, 6, or 8 cysteine residues, and the number of residues can be determined by a relatively simple mass spectrometry experiment. We show here that the prior knowledge of the number of cysteines in a precursor ion is highly advantageous for de novo sequencing.

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Author information

Authors and Affiliations

  1. Palo Alto Research Center, USA

    Swapnil Bhatia, Yong J. Kil & Marshall Bern

  2. Department of Electrical and Computer Engineering, Boston University, USA

    Swapnil Bhatia

  3. Rockefeller University, USA

    Beatrix Ueberheide & Brian Chait

  4. Mapua Institute of Technology, The Philippines

    Lemmuel L. Tayo

  5. Marine Science Institute, University of the Philippines, The Philippines

    Lemmuel L. Tayo & Lourdes J. Cruz

  6. The Scripps Research Institute, USA

    Bingwen Lu & John R. Yates III

  7. Pfizer Inc., USA

    Bingwen Lu

Authors
  1. Swapnil Bhatia
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  2. Yong J. Kil
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  3. Beatrix Ueberheide
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  4. Brian Chait
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  5. Lemmuel L. Tayo
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  6. Lourdes J. Cruz
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  7. Bingwen Lu
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  8. John R. Yates III
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  9. Marshall Bern
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Editor information

Editors and Affiliations

  1. EBU3b, University of California San Diego, #4218, 9500 Gilman Drive, 92093-0404, La Jolla, CA, USA

    Vineet Bafna

  2. School of Computing Science, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada

    S. Cenk Sahinalp

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© 2011 Springer-Verlag Berlin Heidelberg

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Bhatia, S. et al. (2011). Constrained De Novo Sequencing of Peptides with Application to Conotoxins. In: Bafna, V., Sahinalp, S.C. (eds) Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science(), vol 6577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20036-6_2

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  • DOI: https://doi.org/10.1007/978-3-642-20036-6_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-20035-9

  • Online ISBN: 978-3-642-20036-6

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