There are between 2-10 billion separate protein molecules per average human cell depending on the cell type, which are encoded by approx. 20000 genes. There is an expansion in the number of different protein species per cell through a number of mechanisms including alternative splicing (potentially 70000 splice variants per cell), millions of potential single nucleotide polymorphisms, plus thousands of possible RNA base modifications within coding regions. Taken together, even before translation has taken place, the potential size of the proteome is vast. Coupled with the post translational processing of proteins through truncation and chemical modifications (enzyme catalysed and otherwise), the potential number of proteoforms in a cell could be in the range of the total number of proteins per cell!
Although it isunlikely that every potential proteoform persists in a cell, the functional expansion of the proteome through the above mechanisms cannot be underestimated. The concept of one gene - one protein - one function is obsolete. Instead we are faced with the unenviable task of identifying the repertoire of proteoforms that are present in cells and ascribing a function to each.
To date only a very small proportion of the proteome is experimentally verified, with a mere 5% of proteins being characterised with greater than 50% coverage, with approx. 10% of the predicted proteome typically yet to be detected by current methodologies. Moreover, only half of the human proteome carries accurate functional predictions, and these rarely take into consideration how different functions may be impacted by subtle changes in sequence, post transcriptional and post translational processing.
Currently commonly used proteomics approaches are limited in capturing the true size of the functioning proteome, and importantly in assigning functions to proteoforms. Shotgun methods have resulted in disconnected information among intact protein species, and the lack of suitable tools means that many rarer PTMs are under sampled. Moreover, smaller proteins are often neglected and generally our ability to identify proteins is only as good as the gene models we have at our disposal
In this presentation, I will present the problems that exist in defining the functional proteome and offer some insights in how we can use existing data and resources to infer function. Finally, I will look to the future to the large scale community efforts required to conquer the functional proteome.