Proteomics of CaCO3 biomineral-associated proteins: How to properly address their analysis

Authors

  • Benjamin Marie,

    Corresponding author
    1. UMR 7245 CNRS/MNHN, Molécules de Communication et d'Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, Paris, France
    • Correspondence: Dr. Benjamin Marie, UMR 7245 CNRS MCAM, Muséum National d'Histoire Naturelle, 12 rue Buffon CP39, 75005 Paris, France

      E-mail: bmarie@mnhn.fr

      Fax: +33-1-40-79-31-35

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  • Paula Ramos-Silva,

    1. UMR 6282 CNRS/uB, Biogéosciences, Université de Bourgogne, Dijon, France
    2. Section Computational Science, Informatics Institute, Universiteit van Amsterdam, Amsterdam, The Netherlands
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  • Frédéric Marin,

    1. UMR 6282 CNRS/uB, Biogéosciences, Université de Bourgogne, Dijon, France
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  • Arul Marie

    1. UMR 7245 CNRS/MNHN, Plateforme de Spectrométrie de Masse et de Protéomique, Muséum National d'Histoire Naturelle, Paris, France
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Abstract

In a recent editorial (Proc. Natl. Acad. Sci., 2013 110, E2144–E2146) and elsewhere, questions have been raised regarding the experimental practices in relation to the proteomic analysis of organic matrices associated to the biomineralized CaCO3 skeletons of metazoans such as molluscan shells and coral skeletons. Indeed, although the use of new high sensitivity MS technology potentially allows to identify a greater number of proteins, it is also equally (or even more) sensitive to contamination of residual proteins from soft tissues, which are in close contact with the biomineral. Based on our own past and present experimental know-how—observations that are reproducible and coherent with the current understanding of extracellular biomineralization processes—we are convinced that a careful and appropriate cleaning of biominerals prior to any analysis is crucial for accurate proteomic investigations and subsequent pertinent interpretation of the results. Our goal is to alert the scientific community about the associated bias that definitely should be avoided, and to provide critical recommendations on sample preparation and experimental design, in order to better take advantage of the aptness of proteomic approaches aiming at improving our understanding of the molecular mechanisms in biomineralization.

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