Method and apparatus for ion fragmentation by electron capture

A mass spectrometer comprising:

• an ion source for generating ions of molecules to be analysed;
• a fragmentation chamber downstream of the ion source, the fragmentation chamber comprising an ion entrance aperture for receiving ions from the ion source, an ion exit aperture for ejecting ions from the fragmentation chamber, a magnet, and an electron source arranged to generate electrons for direction into the fragmentation chamber, the fragmentation chamber being arranged to trap ions that have entered through the ion entrance aperture within a volume V, the electrons from the electron source being directed towards the volume V so as to irradiate the trapped ions in the presence of the magnetic field generated by the magnet, in order to cause dissociation;
• and,
• a mass analyser, arranged to receive ions generated by the ion source and configured to mass filter the ions prior to ejection to the fragmentation chamber, the mass analyzer being further arranged to receive the fragment ions that have been ejected from the ion exit aperture of the fragmentation chamber.

A method of generating fragment ions by electron capture, comprising:

• (a) directing the ions to be fragmented into a fragmentation chamber of a mass spectrometer arrangement through an ion entrance aperture of the fragmentation chamber;
• (b) trapping at least some of the ions to be fragmented in at least one direction of the fragmentation chamber by using a magnetic field, the ions being trapped within a volume V;
• (c) generating an electron beam using an electron source located away from the volume V;
• (d) irradiating the trapped ions in the volume V with the electrons generated by the electron source in the presence of the said magnetic field, so as to cause dissociation;
• and
• (e) ejecting the resultant fragment ions from the fragmentation chamber through an ion exit aperture thereof and receiving and trapping the ejected fragment ions in the first ion trapping device for subsequent analysis at a different location away from the fragmentation chamber, wherein the ion entrance aperture and ion exit aperture are separate and formed adjacent each other on a common face of the fragmentation chamber.