Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome

Better understanding how cells are regulated and adapt to their environment based on the reversible phosphorylation of proteins is a key question of current molecular and systems biology research. In this study, an advanced mass spectrometry based approach leveraging the electron transfer dissociation (ETD) technique in combination with CID using a linear ion trap mass spectrometer is described. The technique was applied, for the first time, to the identification of phosphorylated peptides isolated from the Drosophila melanogaster Kc167 cell line. We demonstrate that the method is particularly useful for the characterization of large phosphopeptides, including those with multiple phosphorylation sites, as extensive series of c' and z fragment-ions were observed. Finally, we have applied a directed tandem mass spectrometric workflow using inclusion lists to increase the number of identified peptides.