Curr Biol. 2014 Jul 7;24(13):1467-75.

Title: Deep Proteomics of the Xenopus laevis Egg using an mRNA-Derived Reference Database.

Wuehr M, Freeman RM Jr, Presler M, Horb ME, Peshkin L, Gygi SP, Kirschner MW.

Abstract:

BACKGROUND:
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.