Protein phosphorylation, a reversible post-translational modification, has been long identified as a critical regulator in a growing number of cellular processes. Most notably, phosphorylation has been implicated in the signal transduction pathways regulating the cell cycle, cellular proliferation, differentiation, and gene expression events. The ubiquitous nature of phosphorylation as a control mechanism has led to the study of phosphoproteomics. However, lack of universally employed strategies in the enrichment, identification, and characterization of phosphoproteins has hindered the feasibility of elucidating a complete phosphoproteome. Currently, antibodies that recognize either a single phosphorylated amino acid residue or an entire phospho-specific motif are available. The ability to utilize these antibodies both as functional groups for affinity chromatography and probes in immunodetection procedures makes them a versatile option in phosphoproteomic research. In this article, the procedures commonly used for phosphoproteomic analysis will be reviewed, with a major focus on present developments and future challenges using phospho-specific antibodies for phosphoproteome explorations.