High accuracy mass spectrometry in large-scale analysis of protein phosphorylation.

With the appearance of a new generation of high-performance hybrid mass spectrometers, high accuracy (sub-parts-per-million) mass spectrometry is becoming increasingly available to a wider scientific community. Here we discuss the advantages of such mass spectrometric instrumentation in the global analysis of protein phosphorylation. We describe a detailed workflow for fractionation and enrichment of phosphopeptides from digests of whole cell/tissue lysates by strong cation exchange and TiO(2) chromatography and their subsequent measurement on an LTQ-Orbitrap mass spectrometer under several acquisition regimes.