Peptide-based phosphoproteomics with immobilized metal ion chromatography

The identification of protein phosphorylation sites has always been a challenging task, traditionally involving large amounts of radioactive phosphorus and high-performance liquid chromatography separation and Edman sequencing of phosphopeptides. The rapid development of mass spectrometric methods has advanced protein research significantly, and the identification of in vivo post-translational modifications of even rare proteins is now possible. Even with the new generation of machines, however, phosphopeptides do not lend themselves easily to mass spectrometric analysis. In complex mixtures of peptides, phosphopeptides are often difficult to detect because of suppression effects during ionization. This problem can be largely solved by affinity purification/enrichment of the phosphopeptides, and immobilized metal ion affinity chromatography (IMAC) on chelated Fe3+ or other metal ions has emerged as the simplest and most useful method. IMAC has been useful to identify several in vivo phosphorylation sites of individual proteins, but is easier to apply to complex mixtures. We describe a complete protocol as it has been used for Arabidopsis plasma membranes, and note where it can be adapted for soluble protein mixtures.