Dereplication and de novo sequencing of nonribosomal peptides (original) (raw)

Nature Methods volume 6, pages 596–599 (2009)Cite this article

Abstract

Nonribosomal peptides (NRPs) are of great pharmacological importance, but there is currently no technology for high-throughput NRP 'dereplication' and sequencing. We used multistage mass spectrometry followed by spectral alignment algorithms for sequencing of cyclic NRPs. We also developed an algorithm for comparative NRP dereplication that establishes similarities between newly isolated and previously identified similar but nonidentical NRPs, substantially reducing dereplication efforts.

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Figure 1: Experimental and theoretical spectra of seglitide.

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Acknowledgements

We thank G. Kucherov for many helpful discussions and members of the Norine team for helping with the Norine database; D. Meluzzi for the help in the data collection process; B. Moore (Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego) and A. Schultz (Scripps Institution of Oceanography, University of California, San Diego) for providing the cyclomarin compounds, and W. Fenical (Scripps Institution of Oceanography, University of California, San Diego) and K. Maloney (Scripps Institution of Oceanography, University of California, San Diego) for providing compound 879. This project was supported by US National Institutes of Health grants 1-P41-RR024851-01, GM086283 and cA10u851, and by the PhRMA foundation.

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Author notes

  1. Julio Ng and Nuno Bandeira: These authors contributed equally to this work.

Authors and Affiliations

  1. Bioinformatics Program, University of California San Diego, La Jolla, California, USA
    Julio Ng
  2. Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    Nuno Bandeira & Pavel A Pevzner
  3. Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
    Wei-Ting Liu, Majid Ghassemian & Pieter C Dorrestein
  4. Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
    Thomas L Simmons & William H Gerwick
  5. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
    William H Gerwick & Pieter C Dorrestein
  6. Department of Chemistry, University of California Santa Cruz, Santa Cruz, California, USA
    Roger Linington

Authors

  1. Julio Ng
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  2. Nuno Bandeira
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  3. Wei-Ting Liu
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  4. Majid Ghassemian
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  5. Thomas L Simmons
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  6. William H Gerwick
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  7. Roger Linington
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  8. Pieter C Dorrestein
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  9. Pavel A Pevzner
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Corresponding author

Correspondence toPavel A Pevzner.

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Ng, J., Bandeira, N., Liu, WT. et al. Dereplication and de novo sequencing of nonribosomal peptides.Nat Methods 6, 596–599 (2009). https://doi.org/10.1038/nmeth.1350

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