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Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a post-translational modification. Phosphorylation is a key reversible modification that regulates protein function, subcellular localization, complex formation, degradation of proteins and therefore cell signalling networks. With all of these modification results, it is assumed that up to 30% of all proteins may be phosphorylated, some multiple times.
Compared to expression analysis, phoshoproteomics provides two additional layers of information. First, it provides clues on what protein or pathway might be activated because a change in phosphorylation status almost always reflects a change in protein activity. Second, it indicates what proteins might be potential drug targets as exemplified by the kinase inhibitor Gleevec. While phosphoproteomics will greatly expand knowledge about the numbers and types of phosphoproteins, its greatest promise is the rapid analysis of entire phosphorylation based signalling networks.
Additional recommended knowledge
Overview of Phosphoproteomic Analysis
A sample large-scale phosphoproteomic analysis includes
Tools and Methods
The analysis of the entire complement of phosphorylated proteins in a cell is certainly a feasible option. This is due to the optimization of enrichment protocols for phosphoproteins and phosphopeptides, better fractionation techniques using chromatography, and improvement of methods to selectively visualize phosphorylated residues using mass spectrometry. Although the current procedures for phosphoproteomic analysis are greatly improved, there is still sample loss and inconsistencies with regards to sample preparation, enrichment , and instrumentation. Bioinformatics tools and biological sequence databases are also necessary for high-throughput phosphoproteomic studies.
Mass Spectrometry Analysis
Phosphoproteomics in the Study of Signal Transduction
Intracellular signal transduction is primarily mediated by the reversible phosphorylation of various signalling molecules by enzymes dubbed kinases. Kinases transfer phosphate groups from ATP to specific serine, threonine or tyrosine residues of target molecules. The resultant phosphorylated protein may have altered activity level, subcellular localization or tertiary structure.
Phosphoproteomic analyses are ideal for the study of the dynamics of signalling networks. In one study design, cells are exposed to SILAC labelling and then stimulated by a specific growth factor. The cells are collected at various timepoints, and the lysates are combined for analysis by tandem MS. This allows experimenters to track the phosphorylation state of many phosphoproteins in the cell over time. The ability to measure the global phosphorylation state of many proteins at various time points makes this approach much more powerful than traditional biochemical methods for analyzing signalling network behavior.
One study was able to simultaneously measure the fold-change in phosphorylation state of 127 proteins between unstimulated and EphrinB1-stimulated cells. Of these 127 proteins, 40 showed increased phosphorylation with stimulation by EphrinB1. The researchers were able to use this information in combination with previously published data to construct a signal transduction network for the proteins downstream of the EphB2 receptor.
Another recent phosphoproteomic study included large-scale identification and quantification of phosphorylation events triggered by the anti-diuretic hormone vasopressin in kidney collecting duct.  A 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).
Phosphoproteomics in the Study of Cancer
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.
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.
|This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Phosphoproteomics". A list of authors is available in Wikipedia.|