Experiment: A new general phosphatase inhibitor was used to treat a SILAC heavy labeled cell line. Phosphopeptides were enriched by the three stage method outlined in my methods book. LC-MS analysis was performed with CID neutral loss MS/MS with optional ETD activation of the phosphopeptides that were large (z=3, >900; z=4, >750, all ions z>=5; the default Xcalibur supplemental fragmentation method)
Post-processing we looked at the number of phosphopeptides that were identified by each method that were interesting (differentially regulated >2.0 fold).
Here's how it breaks down:
Summary: If you have ETD on your Orbitrap, even though it is a pain to clean and tune, using it to supplement CID may double the number of interesting phosphorylation events.