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EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning

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Research in Computational Molecular Biology (RECOMB 2005)

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

Abstract

We report on a new de novo peptide sequencing algorithm that uses spectral graph partitioning. In this approach, relationships between m/z peaks are represented by attractive and repulsive springs, and the vibrational modes of the spring system are used to infer information about the peaks (such as “likely b-ion” or “likely y-ion”). We demonstrate the effectiveness of this approach by comparison with other de novo sequencers on test sets of ion-trap and QTOF spectra, including spectra of mixtures of peptides. On all data sets we outperform the other sequencers. Along with spectral graph theory techniques, EigenMS incorporates another improvement of independent interest: robust statistical methods for recalibration of time-of-flight mass measurements. Robust recalibration greatly outperforms simple least-squares recalibration, achieving about three times the accuracy for one QTOF data set.

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Authors and Affiliations

  1. Palo Alto Research Center, 3333 Coyote Hill Rd., Palo Alto, CA, 94304, USA

    Marshall Bern & David Goldberg

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  1. Marshall Bern
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  2. David Goldberg
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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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Bern, M., Goldberg, D. (2005). EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. 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_27

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  • DOI: https://doi.org/10.1007/11415770_27

  • 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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