Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Mingxun Wang, Jeremy J. Carver, Pavel Pevzner, Hosein Mohiman, Nuno Bandeira, Vanessa V. Phelan, Laura M. Sanchez, Neha Garg, Jeramie Watrous, Tal Luzzatto-Knaa, Charlotte Frydenlund Michelsen, Lars Jelsbak, Maria Månsson, Andreas Klitgaard, Kristian Fog Nielsen

    Research output: Contribution to journalJournal articleResearchpeer-review

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    Abstract

    The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
    Original languageEnglish
    JournalNature Biotechnology
    Volume34
    Issue number8
    Pages (from-to)828-837
    Number of pages10
    ISSN1087-0156
    DOIs
    Publication statusPublished - 2016

    Bibliographical note

    For full list of authors, see the publication.

    Keywords

    • Computational platforms and environments
    • Mass spectrometry

    Cite this

    Wang, M., Carver, J. J., Pevzner, P., Mohiman, H., Bandeira, N., Phelan, V. V., ... Nielsen, K. F. (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34(8), 828-837. https://doi.org/10.1038/nbt.3597
    Wang, Mingxun ; Carver, Jeremy J. ; Pevzner, Pavel ; Mohiman, Hosein ; Bandeira, Nuno ; Phelan, Vanessa V. ; Sanchez, Laura M. ; Garg, Neha ; Watrous, Jeramie ; Luzzatto-Knaa, Tal ; Frydenlund Michelsen, Charlotte ; Jelsbak, Lars ; Månsson, Maria ; Klitgaard, Andreas ; Nielsen, Kristian Fog. / Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. In: Nature Biotechnology. 2016 ; Vol. 34, No. 8. pp. 828-837.
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    abstract = "The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.",
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    author = "Mingxun Wang and Carver, {Jeremy J.} and Pavel Pevzner and Hosein Mohiman and Nuno Bandeira and Phelan, {Vanessa V.} and Sanchez, {Laura M.} and Neha Garg and Jeramie Watrous and Tal Luzzatto-Knaa and {Frydenlund Michelsen}, Charlotte and Lars Jelsbak and Maria M{\aa}nsson and Andreas Klitgaard and Nielsen, {Kristian Fog}",
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    Wang, M, Carver, JJ, Pevzner, P, Mohiman, H, Bandeira, N, Phelan, VV, Sanchez, LM, Garg, N, Watrous, J, Luzzatto-Knaa, T, Frydenlund Michelsen, C, Jelsbak, L, Månsson, M, Klitgaard, A & Nielsen, KF 2016, 'Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking', Nature Biotechnology, vol. 34, no. 8, pp. 828-837. https://doi.org/10.1038/nbt.3597

    Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. / Wang, Mingxun; Carver, Jeremy J.; Pevzner, Pavel; Mohiman, Hosein; Bandeira, Nuno; Phelan, Vanessa V.; Sanchez, Laura M.; Garg, Neha; Watrous, Jeramie; Luzzatto-Knaa, Tal; Frydenlund Michelsen, Charlotte; Jelsbak, Lars; Månsson, Maria; Klitgaard, Andreas; Nielsen, Kristian Fog.

    In: Nature Biotechnology, Vol. 34, No. 8, 2016, p. 828-837.

    Research output: Contribution to journalJournal articleResearchpeer-review

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    AU - Wang, Mingxun

    AU - Carver, Jeremy J.

    AU - Pevzner, Pavel

    AU - Mohiman, Hosein

    AU - Bandeira, Nuno

    AU - Phelan, Vanessa V.

    AU - Sanchez, Laura M.

    AU - Garg, Neha

    AU - Watrous, Jeramie

    AU - Luzzatto-Knaa, Tal

    AU - Frydenlund Michelsen, Charlotte

    AU - Jelsbak, Lars

    AU - Månsson, Maria

    AU - Klitgaard, Andreas

    AU - Nielsen, Kristian Fog

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    AB - The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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