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Metastable fragmentation of modified peptides during matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has been investigated. Fragment ions of modified peptides generated by metastable loss of modification-specific neutral fragments have been detected by MALDI mass spectrometry in the reflector mode. Peptides acetylated at their N-terminus exhibit a characteristic loss of CH2CO from the acetyl group. Serine and threonine phosphopeptides typically show metastable loss of H3PO4 and to a minor extent of HPO3 in both the continuous and delayed extraction mode. Tyrosine phosphopeptides generally show a loss of HPO3 of moderate abundance. For methionine sulfoxide containing peptides metastable loss of methanesulfenic acid is observed. The extent of this fragmentation is reduced when the analysis is performed with delayed extraction. However, delayed extraction facilitates the recognition of metastable fragment ion signals, since signals of intact molecular ions exhibit a significantly higher resolution than signals generated by metastable fragmentation. In complex mixtures precursor ion selection supports the correlation between the molecular ions of modified peptides and their characteristic fragment ions generated by metastable decomposition.
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