FRAGMENTATION OF PHOSPHOPEPTIDES IN AN ION-TRAP MASS-SPECTROMETER

A systematic study of the fragmentation pattern of phosphopeptides in an electrospray (ESI) ion trap mass spectrometer is presented. We show that phosphotyrosine- and phosphothreonine-containing peptides show c omplicated fragmentation patterns. These phosphopeptides were observed to lose the phosphate moiety in the form of H3PO4 and/or HPO3, but we re also detected with no loss of the phosphate group. The tendency to lose the phosphate moiety depends strongly on the charge state. Thus, the highest observed charge state tends to retain the phosphate moiety with extensive fragmentation along the peptide backbone. We also show that phosphoserine-containing peptides have relatively simple fragmen tation patterns of losing H3PO4. This loss is independent of the charg e state. We suggest strategies for the accurate identification of phos phorylation sites using the ion trap mass spectrometer. (J Am Soc Mass Spectrom 1998, 9, 1175-1188) (C) 1998 American Society for Mass Spect rometry.