Accelerated Articles Electron Capture Dissociation in a Radio Frequency Ion Trap Takashi Baba,* Yuichiro Hashimoto, Hideki Hasegawa, Atsumu Hirabayashi, and Izumi Waki Central Research Laboratory, Hitachi, Ltd., Kokubunji, Tokyo 185-8601, Japan We report on the first evidence of electron capture dissociation (ECD) in a radio frequency (rf) ion trap. Peptide ions, [substance P] 2 + , trapped in a two-dimen- sional, linear rf ion trap were cleaved by electrons injected along the central axis of the trap. Along the axis, the rf field component was zero and a magnetic field of 50 mT was applied. This electron injection scheme keeps the energy of the electrons below 1 eV, preventing them from heating by the rf field. The present ECD efficiency is ∼4% by irradiation of electron current of 0.2 μA for 80 ms. ECD in rf traps may open high-throughput and low-cost ECD applications to obtain molecular structure informa- tion complementary to collision-induced dissociation. Electron capture dissociation (ECD) is a powerful tool for structure analysis of biomolecules, such as peptides, proteins, and their posttranslationally modified products, 1-3 because it allows adiabatic, nonergodic fragmentation at c sites and z sites of peptides. It is complementary to collision-induced dissociation and infrared multiphoton dissociation, which contain adiabatic b site and y site fragmentation. Because ECD reaction cross sections are small (typically 10 -15 m 2 ) and they have the maximum at low electron kinetic energy of sub 1 eV 3 , Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry has been the only technique that has enabled practical ECD to date. Long interaction time and low-energy electrons are achieved by FT- ICR because it traps precursor ions by a static electromagnetic field so that heating of electrons by time-varying electromagnetic field is avoided. 1 ECD in radio frequency (rf) traps, which are small systems without superconducting magnets, has been a challenging target in order to develop low cost and easily operated ECD devices. 1,4-6 Vachet et al. reported that ECD was not observed when electrons were injected into a three-dimensional radio frequency-quadrupole (RFQ) ion trap, or Paul trap, in 1995, because the electrons were energized, or heated, by the rf field. 4 Recently, Ivonin and Zubarev showed, by computer simulation, 5 the feasibility of ECD using a Paul trap with a weak magnetic field. Baba et al. proposed and tested an ECD device that used a three-dimensional static electromagnetic trap (Penning trap) without success. 6 This paper reports the first evidence of ECD in an rf ion trap, which was enabled by a newly designed rf-ECD cell that avoids heating of electrons. Concept of rf-ECD Cell. Our ECD mass spectrometer shown in Figure 1 contains the following two items; (1) an ECD reaction device, i.e., an ECD cell composed of a linear rf ion trap combined with a magnetic field, and (2) a mass analyzer separated from the ECD cell. A linear rf ion trap in the ECD cell for ion confinement consists of a two-dimensional radio frequency electric field in the radial direction, or x and y direction, and a static electric field in the axial direction, or z direction. To avoid perturbation by the ion trap rf field, or rf heating, electrons are injected along the z axis, in which direction the rf field is zero. In addition, a magnetic field is applied in the trap parallel to the z axis of the linear rf trap to confine electrons along the z axis. The magnetic field of ∼0.1 T is used to obtain high transmission efficiency of electrons and to avoid the heating of electrons by the ion trap rf field. The rf * To whom correspondence should be addressed. E-mail: baba@ harl.hitachi.co.jp. Telephone: +81-42-323-1111 ext 3911. Fax: +81-42-327-7807. (1) Zubarev, R. A. Curr. Opin. Biotechnol. 2004 , 15, 12-16. (2) Taybin, Y. O.; Hakanson, P.; Budnik, B. A.; Haselmann, K. F.; Kjeldsen, F.; Gorshkov, M.; Zubarev, R. A. Rapid Commun. Mass Spectrom. 2001 , 15, 1849-1854. (3) Zubarev, R. A.; Horn, D. M.; Fridriksson, E. K.; Kelleher, N. L.; Kruger, N. A.; Lewis, M. A.; Carpenter, B. K.; McLafferty, F. W. Anal. Chem. 2000 , 72, 563. (4) Vachet, R. W.; Clark, S. D.; Glish, G. L. Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, 1995; p 1111. (5) Ivonin, I.; Zubarev, R. A. Proceedings of the 51st ASMS Conference on Mass Spectrometry and Allied Topics, 2003; ThPE057. (6) Baba, T.; Black, D. M.; Glish, G. L. Proceedings of the 51st ASMS Conference on Mass Spectrometry and Allied Topics, 2003; ThPJ1 165. Anal. Chem. 2004, 76, 4263-4266 10.1021/ac049309h CCC: $27.50 © 2004 American Chemical Society Analytical Chemistry, Vol. 76, No. 15, August 1, 2004 4263 Published on Web 07/02/2004