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.
Enrichment Strategies
Previous procedures to isolate phosphorylated proteins included radioactive labeling with 32P-labeled ATP followed by SDS polyacrylamide gel electrophoresis or thin layer chromatography. These traditional methods are inefficient because it is impossible to obtain large amounts of proteins required for phosphorylation analysis. Therefore, the current and simplest methods to enrich phosphoproteins are affinity purification using phosphospecific antibodies, immobilized metal affinity chromatography (IMAC), strong cation exchange (SCX) chromatography, or titanium dioxide chromatography. Antiphosphotyrosine antibodies have been proven very successful in purification, but fewer reports have been published using antibodies against phosphoserine- or phosphothreonine-containing proteins. IMAC enrichment is based on phosphate affinity for immobilized metal chelated to the resin. SCX separates phosphorylated from non-phosphorylated peptides based on the negatively charged phosphate group. Titanium dioxide chromatography is a newer technique that requires significantly less column preparation time. Many phosphoproteomic studies use a combination of these enrichment strategies to obtain the purest sample possible.
Mass Spectrometry Analysis
Mass spectrometry is currently the best method to adequately compare pairs of protein samples. The two main procedures to perform this task are using isotope-coded affinity tags (ICAT) and stable isotopic amino acids in cell culture (SILAC). In the ICAT procedure samples are labeled individually after isolation with mass-coded reagents that modify cysteine residues. In SILAC, cells are cultured separately in the presence of different isotopically labeled amino acids for several cell divisions allowing cellular proteins to incorporate the label. Mass spectrometry is subsequently used to identify phosphoserine, phosphothreonine, and phosphotyrosine-containing peptides.
Read more about this topic: Phosphoproteomics
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