A pulsed dual electrospray ionization source has been developed to generate positive and negative ions for subsequent ion/ion reaction experiments. The two sprayers, typically a nano-electrospray emitter for analytes and an electrospray emitter for reagents, are positioned in a parallel fashion close to the sampling orifice of a triple quadrupole/linear ion trap tandem mass spectrometer (Sciex Q TRAP). The potentials applied to each sprayer are alternately pulsed so that ions of opposite polarity are generated separately in time. Ion/ion reactions take place after ions of each polarity are sequentially injected into a high-pressure linear ion trap, where axial trapping is effected by applying an auxiliary radio frequency voltage to the end lenses. The pulsed dual electrospray source allows optimization of each sprayer and can be readily coupled to any spray interface with no need for instrument modifications, provided the potentials required to transmit the ion polarity of interest can be alternated in synchrony with the emitter potentials. Ion/ion reaction examples such as charge reduction of multiply charged protein ions, charge inversion of peptides ions, and protein-protein complex formation are given to illustrate capabilities of the pulsed dual electrospray source in the study of gas-phase ion/ion chemistry. T he advent of electrospray ionization (ESI) mass spectrometry has revolutionized the analysis of many biologically important macromolecules [1,2]. Both the polarity and the magnitude of the charge associated with an ionized biomolecule play important roles in the use of tandem mass spectrometry for the identification and structural characterization of the biomolecule from which the ions were derived. Ion/ion reactions provide efficient means for manipulating the identities of gas-phase ions after their initial formation [3,4], including altering ion polarity and absolute charge. Applications of charge manipulation via ion/ ion reactions include: mixture analysis [5][6][7][8], especially with the application of the "ion parking" technique for gas-phase concentration and charge state purification [9], the formation of ions that cannot be directly produced by ESI for subsequent tandem mass spectrometry studies [10], and the reduction of the product ion charge states to singly and doubly charged so as to simplify the interpretation of product ion spectra [11][12][13][14][15][16]. Electron-transfer ion/ion reactions have recently been described as a means of inducing structurally informative dissociation, giving rise to cleavages analogous to those noted in electron capture dissociation [17][18][19][20][21]. In this regard, ion/ion reactions play a role as a probe of primary structure.Electrodynamic ion traps, either a quadrupole ion trap or a linear ion trap (LIT), are particularly useful reaction vessels for ion/ion reactions because of their ability to store oppositely-charged ions simultaneously [22] as well as their ion isolation and MS n functionalities [23]. Most ion/ion reaction studies involving m...