Fig. 7.

Comparison of single-scan (500- to 600-msec) CAD and ETD mass spectra recorded during data-dependent analyses (nHPLC-μESI-MS/MS) of phosphopeptides generated in a tryptic digest of human nuclear proteins. All peptides were converted to methyl esters and subjected to immobilized metal affinity chromatography before analysis by MS. (A) CAD spectrum dominated by fragment ions corresponding to the loss of phosphoric acid and either methanol or water. (B) ETD spectrum containing 13 of 14 possible c- and z-type product ions. Note that the spectrum is devoid of fragment ions corresponding to the loss of phosphoric acid.