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Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP)

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Abstract

The method of protein-based stable isotope probing (protein-SIP) has previously been shown to allow the modeling of carbon fluxes in microbial communities, thus tackling one of the key questions in microbial ecology. The method allows the analysis of stable isotope distribution in peptides, revealing metabolic activities of the species present in an ecosystem. Besides carbon, an application of protein-SIP with nitrogen is of interest for resolving the nitrogen fluxes in microbial communities. Thus, the sensitivity and reliability of a protein-SIP approach employing 15N was analyzed. For this, cultivations of Pseudomonas fluorescens ATCC 17483 with different ratios of 14N/15N were performed, from 10 % down to 0.1 % 15N. After incubation leading to complete labeling of biomass, proteins were extracted and separated by one-dimensional gel electrophoresis, followed by tryptic digest and UPLC Orbitrap MS/MS analysis. 15N relative isotope abundance (RIA) was calculated based on isotopic patterns from identified peptides in mass spectra. Proteomics data have been deposited to ProteomeXchange with identifier PXD000127. The distribution of 15N RIA values among peptides was analyzed in samples with different 15N amount, and potential causes for variations within individual samples of either technical or biological origin were investigated. Using a number of 50 peptides, significant differences (p ≤ 0.05) in 15N incorporation were found between samples of different 15N RIA down to 0.1 %. The study demonstrates that protein-SIP using 15N is sufficiently sensitive for quantitative investigation of microbial activity in nitrogen cycling processes.

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Acknowledgments

We acknowledge the financial support by the Deutsche Forschungsgemeinschaft (SPP 1319) for funding M. Taubert. We are grateful to the excellent technical work of K. Eismann.

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Authors and Affiliations

  1. Department of Proteomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318, Leipzig, Germany

    Martin Taubert, Martin von Bergen & Jana Seifert

  2. School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

    Martin Taubert

  3. Department of Metabolomics, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318, Leipzig, Germany

    Martin von Bergen

  4. Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Sohngaardsholmsvej 49, 9000, Aalborg, Denmark

    Martin von Bergen

  5. Institute of Animal Nutrition, University of Hohenheim, Emil-Wolff-Str. 8, 70599, Stuttgart, Germany

    Jana Seifert

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  1. Martin Taubert
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  2. Martin von Bergen
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  3. Jana Seifert
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Correspondence to Martin Taubert.

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Taubert, M., von Bergen, M. & Seifert, J. Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP). Anal Bioanal Chem 405, 3989–3996 (2013). https://doi.org/10.1007/s00216-013-6828-y

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  • DOI: https://doi.org/10.1007/s00216-013-6828-y

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