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

TitleDeep proteomics of the Xenopus laevis egg using an mRNA-derived reference database.
Publication TypeJournal Article
Year of Publication2014
AuthorsWühr, M, Freeman, RM, Presler, M, Horb, ME, Peshkin, L, Gygi, S, Kirschner, MW
JournalCurr Biol
Volume24
Issue13
Pagination1467-1475
Date Published2014 Jul 07
ISSN1879-0445
KeywordsAnimals, Computational Biology, Databases, Protein, Gene Expression Regulation, Developmental, Internet, Mass Spectrometry, Ovum, Proteins, Proteomics, RNA, Messenger, Xenopus laevis
Abstract

<p><b>BACKGROUND: </b>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.</p><p><b>RESULTS: </b>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.</p><p><b>CONCLUSION: </b>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.</p>

DOI10.1016/j.cub.2014.05.044
Alternate JournalCurr. Biol.
PubMed ID24954049
PubMed Central IDPMC4090281
Grant ListP40OD010997 / OD / NIH HHS / United States
R01 HD073104 / HD / NICHD NIH HHS / United States
R01 DK077197 / DK / NIDDK NIH HHS / United States
R01 GM103785 / GM / NIGMS NIH HHS / United States
R01HD073104 / HD / NICHD NIH HHS / United States
P40 OD010997 / OD / NIH HHS / United States
R01GM103785 / GM / NIGMS NIH HHS / United States
R01DK077197 / DK / NIDDK NIH HHS / United States