Phosphoproteomics - Limitations

Limitations

While phosphoproteomics has greatly expanded knowledge about the numbers and types of phosphoproteins, along with their role in signaling networks, there are still a few limitations to these techniques. To begin with, isolation methods such as anti-phosphotyrosine antibodies do not distinguish between isolating tyrosine-phosphorylated proteins and proteins associated with tyrosine-phosphorylated proteins. Therefore, even though phosphorylation dependent protein-protein interactions are very important, it is important to remember that a protein detected by this method is not necessarily a direct substrate of any tyrosine kinase. Only by digesting the samples before immunoprecipitation can isolation of only phosphoproteins and temporal profiles of individual phosphorylaiton sites be produced. Another limitation is that some relevant proteins will likely be missed since no extraction condition is all encompassing. It is possible that proteins with low stoichiometry of phosphorylation, in very low abundance, or phosphorylated as a target for rapid degradation will be lost.