Deep proteomics of the xenopus laevis egg using an mRNA-derived reference database

Martin Wühr, Robert M. Freeman, Marc Presler, Marko E. Horb, Leonid Peshkin, Steven P. Gygi, Marc W. Kirschner

Research output: Contribution to journalArticle

113 Scopus citations

Abstract

SummaryBackground Mass spectrometry-based proteomics enables the global identification and quantification of proteins and their posttranslational modifications in complex biological samples. However, proteomic analysis requires a complete and accurate reference set of proteins and is therefore largely restricted to model organisms with sequenced genomes. Results Here, we demonstrate the feasibility of deep genome-free proteomics by using a reference proteome derived from heterogeneous mRNA data. We identify more than 11,000 proteins with 99% confidence from the unfertilized Xenopus laevis egg and estimate protein abundance with approximately 2-fold precision. Our reference database outperforms the provisional gene models based on genomic DNA sequencing and references generated by other methods. Surprisingly, we find that many proteins in the egg lack mRNA support and that many of these proteins are found in blood or liver, suggesting that they are taken up from the blood plasma, together with yolk, during oocyte growth and maturation, potentially contributing to early embryogenesis. Conclusion To facilitate proteomics in nonmodel organisms, we make our platform available as an online resource that converts heterogeneous mRNA data into a protein reference set. Thus, we demonstrate the feasibility and power of genome-free proteomics while shedding new light on embryogenesis in vertebrates.

Original languageEnglish (US)
Pages (from-to)1467-1475
Number of pages9
JournalCurrent Biology
Volume24
Issue number13
DOIs
StatePublished - Jul 7 2014
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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    Wühr, M., Freeman, R. M., Presler, M., Horb, M. E., Peshkin, L., Gygi, S. P., & Kirschner, M. W. (2014). Deep proteomics of the xenopus laevis egg using an mRNA-derived reference database. Current Biology, 24(13), 1467-1475. https://doi.org/10.1016/j.cub.2014.05.044