Deep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database

Mass spectrometry based proteomics enables the global identification and quantification of proteins and their post-translational modifications in complex biological samples. Proteomic analysis requires a complete and accurate reference set of proteins, and is therefore largely restricted to model organisms with sequenced genomes. Here, we demonstrate the feasibility of deep genome-free proteomics using a reference proteome derived from heterogeneous mRNA data. We identify more than 11k proteins with 99% confidence from the unfertilized, X. laevis egg and estimate protein abundance with approximately two-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 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. To facilitate proteomics in non-model organisms, we make our platform available as an online resource which 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.