Electron capture dissociation (ECD) allows fragmentation of the phosphopeptide backbone while keeping the labile phospho-amino acid intact. This feature of ECD fragmentation, coupled with the acquisition of mass spectra at high mass accuracy, makes ECD well-suited to phosphorylation mapping. The following methods are designed to focus ECD events on phosphopeptides within a complex peptide sample, either by using phosphoric acid neutral loss peaks as a trigger or by targeted analysis of predetermined precursor masses.
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