Product ion spectral simplification using time-delayed fragment ion capture with tandem linear ion traps

A new technique to generate product ion spectra as the internal energy of a collisionally activated precursor ion evolves is described. The precursor ion is activated by acceleration into a mass-selective linear ion trap under conditions whereby some of the fragment ions formed are unstable within the trap. After a time delay the stability parameters of the ion trap are changed to allow capture of fragments that that were previously unstable. The result is a product ion spectrum that originates from precursor ions with a modified internal energy distribution. It is possible to follow the evolution of the precursor internal energy distribution for many milliseconds after admittance of the precursor ions into the linear ion trap. Time-delayed fragmentation product ion spectra typically display reduced sequential fragmentation products leading to spectra that are more easily interpreted. Several important experimental parameters important to time-delayed fragmentation have been identified and are discussed. The technique has applications for both small precursor ions and multiply charged peptides. Copyright (C) 2003 John Wiley Sons, Ltd.