Mechanistic insights into the multistage gas-phase fragmentation behavior of phosphoserine- and phosphothreonine-containing peptides

The increasing use of multistage tandem mass spectrometry (MS/MS and MS3) methods for comprehensive phosphoproteome analysis studies, as well as the emerging application of in silico spectral intensity prediction algorithms in enhanced database search analysis strategies, necessitate the development of an improved understanding of the mechanisms and other factors that affect the gas-phase fragmentation reactions of phosphorylated peptide ions. To address this need, we have examined the multistage collision-induced dissociation (CID) behavior of a set of singly and doubly charged phosphoserine- and phosphothreonine-containing peptide ions, as-well as their regioselectively or uniformly deuterated derivatives, in a quadrupole ion trap mass spectrometer. Consistent with previous reports, the neutral loss of phosphoric acid (H3PO4) was observed as a dominant reaction pathway upon MS/MS. The magnitude of this loss was found to be highly dependent on the proton mobility of the precursor ion for both phosphoserine- and phosphothreonine-containing peptides. In contrast to that currently accepted in the literature, however, the results obtained in this study unequivocally demonstrate that the loss of H3PO4 does not predominantly occur via a charge-remote beta-elimination reaction. The observation of product ions corresponding to the loss of formaldehyde (CH2O, 30 Da, or CD2O, 32 Da) or acetaldehyde (CH3CHO, 44 Da) upon MS3 dissociation of the [M+nH-H3PO4](n+) product ions from phosphoserine- and phosphothreonine-containing peptide ions, respectively, provide experimental evidence for a charge-directed mechanism involving an S(N)2 neighboring group participation reaction, resulting in the formation of a cyclic product ion. Potentially, these diagnostic MS3 product ions may provide additional information to facilitate the characterization of phosphopeptides containing multiple potential phosphorylation sites.