Internal Fragment Reduction in Top Down ECD Analysis of Proteins

A mass spectrometer, comprising:

• an ion guide for receiving a plurality of precursor ions, and
• an electron capture (ECD) device positioned downstream of said ion guide for receiving at least a portion of the ions exiting said ion guide, said ECD device comprising:
• a first set of L-shaped electrodes arranged in a multipole configuration,
• a second set of L-shaped electrodes arranged in a multiple configuration,
• said first and second electrode sets being positioned relative to one another so as to provide a first channel having a proximal section comprising an inlet for receiving a plurality of precursor ions and having a distal section comprising an outlet through which ions can exit the first channel, and a second channel intersecting the first channel in an electron-ion interaction region in which the precursor ions can interact with the electron beam to generate a plurality of product ions,
• at least one RF power source for application of one or more RF voltages to said first and second electrode sets for providing a radial confinement electromagnetic field for providing radial confinement of the ions,
• one or more auxiliary electrodes positioned relative to said first and second channels to which DC voltages can be applied for guiding the product ions into any of said proximal and distal sections of the first channel and trapping said product and precursor ions therein, and
• an AC excitation signal source for applying an AC excitation to at least one of said first and second electrode sets so as to resonantly excite at least a portion of a plurality of precursor ions trapped in any of the proximal and distal sections to enter said electron-ion interaction.