Abstract: A method and apparatus are provided for providing an ion transmission device or interface between an ion source and a spectrometer. The ion transmission device can include a multipole rod set and includes a damping gas, to damp spatial and energy spreads of ions generated by a pulsed ion source. The multipole rod set has the effect of guiding the ions along an ion path, so that they can be directed into the inlet of a mass spectrometer. The invention has particular application to MALDI (matrix-assisted laser desorption/ionization) ion sources, which produce a small supersonic jet of matrix molecules and ions, which is substantially non-directional, and can have ions travelling in all available directions from the source and having a wide range of energy spreads.

Abstract: A method and apparatus are provided for selective collision-induced dissociation of a substance, by resonance excitation of ions. An ion stream is supplied into a quadrupole ion guide operated at elevated pressure with a buffer gas. In addition to a radio frequency field for guiding ions through the ion guide, an extra field or other excitation is provided. This field is selected to cause resonance excitation of parent ions of interest. These ions gain kinetic energy and undergo enhanced collision-induced dissociation with a buffer gas. This generates fragment ions, so that the resultant ion stream, containing remaining parent ions and fragment ions can be analyzed in a suitable analyzer. The method essentially enables the two steps of selection of a particular parent ion and generation of fragment ions by collision-induced dissociation to be carried out in a single step, giving a simpler apparatus and enhanced efficiency.

Abstract: The invention provides an analytical instrument comprising an affinity capture probe interface, a laser desorption ionization source, and a tandem mass spectrometer. Also presented are new methods for protein discovery and identification and for characterization of molecular interactions that utilize the instrument of the present invention.