Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a posttranslational modification. Phosphorylation is a key reversible modification that regulates protein function, subcellular localization, complex formation, degradation of proteins and therefore cell signaling networks. With all of these modification results, it is estimated that between 30%–65% of all proteins may be phosphorylated, some multiple times. Based on statistical estimates from many datasets, 230,000, 156,000 and 40,000 phosphorylation sites should exist in human, mouse, and yeast, respectively. Compared to expression analysis, phosphoproteomics 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. Overview A sample large-scale phosphoproteomic analysis includes cultured cells undergo SILAC encoding; cells are stimulated with factor of interest (e.g. growth factor, hormone); stimulation can occur for various lengths of time for temporal analysis, cells are lysed and enzymatically digested, peptides are separated using ion exchange chromatography; phosphopeptides are enriched using phosphospecific antibodies, immobilized metal affinity chromatography or titanium dioxide (TiO2) chromatography; phosphopeptides are analyzed using mass spectrometry, and peptides are sequenced and analyzed. 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