The article presents a method for peptide sequence analysis using electron transfer dissociation (ETD) in a radio frequency quadrupole linear ion trap (QLT). The authors modified the QLT to enable ion/ion chemistry, where singly charged anthracene anions transfer electrons to multiply protonated peptides, leading to fragmentation along pathways similar to those observed in electron capture dissociation (ECD). The modifications include the use of a dual isolation waveform to control the ion-trap geometry and the injection of reagent anions and precursor cations. The method was validated through the automated acquisition of high-quality, single-scan ETD MS/MS spectra of phosphopeptides separated by nanoflow HPLC. The results demonstrate that ETD is particularly effective for peptides containing posttranslational modifications (PTMs) and can be used to sequence peptides in complex mixtures. The authors also discuss the potential for combining ETD with other techniques, such as collisional activation dissociation (CAD), to further enhance sequence analysis of intact proteins and large peptides.The article presents a method for peptide sequence analysis using electron transfer dissociation (ETD) in a radio frequency quadrupole linear ion trap (QLT). The authors modified the QLT to enable ion/ion chemistry, where singly charged anthracene anions transfer electrons to multiply protonated peptides, leading to fragmentation along pathways similar to those observed in electron capture dissociation (ECD). The modifications include the use of a dual isolation waveform to control the ion-trap geometry and the injection of reagent anions and precursor cations. The method was validated through the automated acquisition of high-quality, single-scan ETD MS/MS spectra of phosphopeptides separated by nanoflow HPLC. The results demonstrate that ETD is particularly effective for peptides containing posttranslational modifications (PTMs) and can be used to sequence peptides in complex mixtures. The authors also discuss the potential for combining ETD with other techniques, such as collisional activation dissociation (CAD), to further enhance sequence analysis of intact proteins and large peptides.