This article describes a method for analyzing peptide and protein sequences using electron transfer dissociation (ETD) mass spectrometry. The study demonstrates that anthracene anions transfer electrons to multiply protonated peptides in a radio frequency quadrupole linear ion trap (QLT) and induce fragmentation of the peptide backbone along pathways similar to those observed in electron capture dissociation (ECD). Modifications to the QLT instrument are presented that enable this ion/ion chemistry, and automated acquisition of high-quality, single-scan ETD tandem mass spectra of phosphopeptides separated by nanoflow HPLC is described. ECD, introduced six years ago by McLafferty and coworkers, is a method for peptide/protein ion fragmentation that involves the capture of a thermal electron by a protonated peptide, leading to fragmentation of the peptide backbone. ECD is effective for analyzing peptides and proteins with FTICR mass spectrometers, but its most efficient form requires a dense population of near-thermal electrons, which is difficult to achieve in commonly used ion traps. As a result, ECD remains a technique exclusively used with FTICR, the most expensive type of MS instrumentation. In contrast, ETD is a method that uses ion/ion reactions to fragment peptides and proteins. It is independent of amide bond protonation and occurs on a short time scale compared to internal energy distribution. Multiply protonated peptides, and those with posttranslational modifications (PTMs), all fragment more or less randomly along the peptide backbone and are easily sequenced. ETD is particularly well suited for characterization of peptides containing PTMs. The study describes the development of an ETD method for use with a low-cost, widely accessible mass spectrometer such as the QLT. The method involves the use of anions as vehicles for delivering electrons to multiply charged peptide cations. The study also describes the modifications of a QLT mass spectrometer to enable ion/ion experiments, a method of fragmenting multiply protonated peptides, and automated acquisition of high-quality, single-scan ETD tandem mass spectra from phosphopeptides separated by nanoflow HPLC. The study demonstrates that ETD is effective for sequence analysis of peptides and proteins, particularly those containing PTMs. The results show that ETD produces high-quality spectra with good resolution and sensitivity, and that it is particularly useful for analyzing complex mixtures. The study also outlines experiments that use a combination of ion/ion chemistry, CAD, and ETD to characterize the primary structure of intact proteins. Finally, the study suggests that the gas-phase ion/ion chemistry will become an indispensable tool for peptide and protein sequence analysis in the near future and is likely to drive the development of new MS instrumentation and software.This article describes a method for analyzing peptide and protein sequences using electron transfer dissociation (ETD) mass spectrometry. The study demonstrates that anthracene anions transfer electrons to multiply protonated peptides in a radio frequency quadrupole linear ion trap (QLT) and induce fragmentation of the peptide backbone along pathways similar to those observed in electron capture dissociation (ECD). Modifications to the QLT instrument are presented that enable this ion/ion chemistry, and automated acquisition of high-quality, single-scan ETD tandem mass spectra of phosphopeptides separated by nanoflow HPLC is described. ECD, introduced six years ago by McLafferty and coworkers, is a method for peptide/protein ion fragmentation that involves the capture of a thermal electron by a protonated peptide, leading to fragmentation of the peptide backbone. ECD is effective for analyzing peptides and proteins with FTICR mass spectrometers, but its most efficient form requires a dense population of near-thermal electrons, which is difficult to achieve in commonly used ion traps. As a result, ECD remains a technique exclusively used with FTICR, the most expensive type of MS instrumentation. In contrast, ETD is a method that uses ion/ion reactions to fragment peptides and proteins. It is independent of amide bond protonation and occurs on a short time scale compared to internal energy distribution. Multiply protonated peptides, and those with posttranslational modifications (PTMs), all fragment more or less randomly along the peptide backbone and are easily sequenced. ETD is particularly well suited for characterization of peptides containing PTMs. The study describes the development of an ETD method for use with a low-cost, widely accessible mass spectrometer such as the QLT. The method involves the use of anions as vehicles for delivering electrons to multiply charged peptide cations. The study also describes the modifications of a QLT mass spectrometer to enable ion/ion experiments, a method of fragmenting multiply protonated peptides, and automated acquisition of high-quality, single-scan ETD tandem mass spectra from phosphopeptides separated by nanoflow HPLC. The study demonstrates that ETD is effective for sequence analysis of peptides and proteins, particularly those containing PTMs. The results show that ETD produces high-quality spectra with good resolution and sensitivity, and that it is particularly useful for analyzing complex mixtures. The study also outlines experiments that use a combination of ion/ion chemistry, CAD, and ETD to characterize the primary structure of intact proteins. Finally, the study suggests that the gas-phase ion/ion chemistry will become an indispensable tool for peptide and protein sequence analysis in the near future and is likely to drive the development of new MS instrumentation and software.