Pros and cons of the most useful phosphoproteomic -MS based tools. Generally, immunoprecipitation of Tyrosine via antibodies, is more efficient than antibody immunoprecipitation of Serine and Threonine residues. On the other hand, affinity chromatography of IMAC and TiO2, is more efficient for isolating phosphorylated residues of Serine and Threonine than Tyrosine. Moreover, TiO2 has shown higher specificity when it is coupled to DHB than IMAC. In addition, IMAC has shown higher specificity when converting non-phosphorylated residues (acidic peptides) to methyl esters, but the complexity of spectra increases. Furthermore, SCX, SAX and calcium phosphate precipitation methods, are more efficient when coupled to IMAC and/or TiO2 for clinical phosphoproteomic studies.