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. In collaboration, the Gygi and Kirschner labs demonstrated the feasibility of deep genome-free proteomics by using a reference proteome derived from heterogeneous mRNA data. They identify more than 11,000 proteins from the egg of the African clawed frog and estimate each protein's abundance with approximately 2-fold precision. To facilitate proteomics in nonmodel organisms, the researchers made their platform available as an online resource that converts heterogeneous mRNA data into a protein reference set.  This work was published in Current Biology.

Figure: Xenopus laevis ovary