Utility of reaction intermediate monitoring with photodissociation multi-stage (MSn) time-of-flight mass spectrometry for mechanistic and structural studies: Phosphopeptides

Abstract

In tandem mass spectra of phosphopeptides, intact sequence ions are often missing or appear weakly. Instead, dephosphorylated sequence ions appear prominently. In this work, we used photodissociation (PD) multi-stage (MSn) time-of-flight mass spectrometry that can monitor reaction intermediates with lifetime as short as 100 ns to study the formation of dephosphorylated sequence ions such as yn-H3PO4. yn-H3PO4 was found to be formed mainly by H3PO4 loss from yn. For doubly phosphorylated peptides, yn seemed to lose H3PO4 stepwise and form yn-H3PO4 and yn-2H3PO4. Even when yn was absent in PD-MS2 spectrum, its m/z could be predicted from those of yn-H3PO4 and/or yn-2H3PO4. Complete sequence coverage was possible when the data from PD-MS2 and PD-MS3 were combined, demonstrating the utility of transient ion detection by PD-MS3 for structure analysis.