total of 714 phosphorylation sites on 223 unique phosphoproteins were identified, including three novel phosphorylation sites in the vasopressin-sensitive water channel aquaporin-2 (AQP2). Cancer research Since the inception of phosphoproteomics, cancer research has focused on changes to the phosphoproteome during tumor development. Phosphoproteins could be cancer markers useful to cancer diagnostics and therapeutics. In fact, research has shown that there are distinct phosphotyrosine proteomes of breast and liver tumors. There is also evidence of hyperphosphorylation at tyrosine residues in breast tumors but not in normal tissues. Findings like these suggest that it is possible to mine the tumor phosphoproteome for potential biomarkers. Increasing amounts of data are available suggesting that distinctive phosphoproteins exist in various tumors and that phosphorylation profiling could be used to fingerprint cancers from different origins. In addition, systematic cataloguing of tumor-specific phosphoproteins in individual patients could reveal multiple causative players during cancer formation. By correlating this experimental data to clinical data such as drug response and disease outcome, potential cancer markers could be identified for diagnosis, prognosis, prediction of drug response, and potential drug targets. Limitations While phosphoproteomics has greatly expanded knowledge about the numbers and types of phosphoproteins, along with their role in signaling networks, there are still several 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 phosphorylation 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. Bioinformatics analyses of low-throughput phosphorylation data together with high-throughput phosphoproteomics data (based mostly on MS/MS) estimate that current high-throughput protocols, after several repetitions are capable of capturing 70% to 95% of total phosphoproteins, but only 40% to 60% of total phosphorylation sites. See also Glycoproteomics References External links Phosida Phosphorylation Site Database Analysis of Signal Transduction YouTube Video CDPD Collecting Duct Phosphoprotein Database Biotechnology