An ion spectrometer is provided, comprising: an ion source, arranged to generate ions continuously with a first range of mass to charge ratios; and an ion trap, arranged to receive ions from the ion source along an axis, and to eject ions with a second range of mass to charge ratios orthogonally to that axis, the second range of mass to charge ratios being narrower than the first range of mass to charge ratios. In some embodiments, ions generated by the ion source continuously flow into the ion trap. Additionally or alternatively, ion optics receive ions ejected from the ion trap and cool the ions without substantial fragmentation. An ion analyser receives ions ejected from the ion trap or ion optics and separates the ions in accordance with at least one characteristic of the ions.

A method for characterising ions includes trapping a first-generation ions in an ion trap; cooling the plurality of first-generation ions; photo-fragmenting the plurality of cooled first generation ions to obtain a plurality of second-generation ions, the second-generation ions being different to the first-generation ions, the plurality of second-generation ions being at least of one first type; selecting the first type of second-generation ions in the ion trap by ejecting, out of the trap, any residual first-generation ion and any second-generation ion of a type different from the first type; cooling the second-generation ions of the first type selected and trapped in the trap; photo-fragmenting the cooled second-generation ions of the first type to obtain a plurality of third-generation ions, the plurality of third-generation ions being different from the plurality of second-generation ions, the plurality of third-generation ions being at least of one first type; detecting the plurality of last-generation ions.

A device and associated method are disclosed for interfacing an ion trap to a pulsed mass analyzer (such as a time-of-flight analyzer) in a mass spectrometer. The device includes a plurality of separate confinement cells and structures for directing ions into a selected one of the confinement cells. Ions are ejected from the ion trap in a series of temporally successive ion packets. Each ion packet (which may consist of ions of like mass-to-charge ratio), is received by the ion interface device, fragmented to form product ions, and then stored and cooled in the selected confinement cell. Storage and cooling of the ion packet occurs concurrently with the receipt and storage of at least one later-ejected ion packet. After a predetermined cooling period, the ion packet is released to the mass analyzer for acquisition of a mass spectrum.

An ion spectrometer is provided, comprising: an ion source, arranged to generate ions continuously with a first range of mass to charge ratios; and an ion trap, arranged to receive ions from the ion source along an axis, and to eject ions with a second range of mass to charge ratios orthogonally to that axis, the second range of mass to charge ratios being narrower than the first range of mass to charge ratios. In some embodiments, ions generated by the ion source continuously flow into the ion trap. Additionally or alternatively, ion optics receive ions ejected from the ion trap and cool the ions without substantial fragmentation. An ion analyser receives ions ejected from the ion trap or ion optics and separates the ions in accordance with at least one characteristic of the ions.

An ion spectrometer is provided, comprising: an ion source, arranged to generate ions continuously with a first range of mass to charge ratios; and an ion trap, arranged to receive ions from the ion source along an axis, and to eject ions with a second range of mass to charge ratios orthogonally to that axis, the second range of mass to charge ratios being narrower than the first range of mass to charge ratios. In some embodiments, ions generated by the ion source continuously flow into the ion trap. Additionally or alternatively, ion optics receive ions ejected from the ion trap and cool the ions without substantial fragmentation. An ion analyser receives ions ejected from the ion trap or ion optics and separates the ions in accordance with at least one characteristic of the ions.

A first mass analysis is executed in a condition that gas is not introduced into a loop-flight chamber (4), and a time-of-flight spectrum obtained in a data processor (12) is stored in a storage unit (13). Next, a second mass analysis is executed on the same sample as the one used in the first mass analysis in a condition that a valve (8) is opened and helium gas (He) is introduced into the loop-flight chamber (4), and the time-of-flight spectrum is obtained in the data processor (12). If different kinds of ions having the same m/z value exit, these ions form a single peak in the first time-of-flight spectrum, while these ions appear as separate peaks in the second time-of-flight spectrum even though they have the same m/z value. This is because, in the second mass analysis, the ions collide with the gas and have different times of flight depending on their difference in size. A spectrum comparator (14) judges a change in the position or shape of the peak by comparing the two spectra, and outputs information relating to the difference in the size of the ions (the molecular structure, charge state, or molecular class of the ions), and the like. Accordingly, a wider variety of information than ever before can be provided.

A method of ejecting ions to be analyzed from a quadrupole ion trap in which a trapping field is created by one or more RF voltages applied to one or more electrodes of the trap, the method comprising the steps of cooling the ions to be analyzed within the quadrupole ion trap until the ions are thermalized, reducing the amplitude of one or more RF voltages applied to the quadrupole ion trap and applying the reduced amplitude RF voltages for one half cycle after the one or more RF voltages have reached a zero crossing point, turning off the RF voltages applied to the quadrupole ion trap, and ejecting the ions to be analyzed from the quadrupole ion trap.

A method for mass spectrometric analysis of a peptide having at least one fragile moiety includes using electrospray ionization to generate a negatively charged ion of said peptide, trapping and cooling the negatively charged peptide ion in a radiofrequency (RF) ion trap containing a cooling buffer gas, and exposing said cooled, trapped peptide ion to an electron beam so as to cause negative electron activated dissociation (negative EAD) of the negatively charged peptide ion to generate a plurality of fragment ions.

In some examples, an ion funnel-based collision cell may include an ion funnel entrance section formed by a plurality of adjacently disposed entrance members. Each entrance member of at least one pair of the adjacently disposed entrance members may include a successively larger opening to form a tapered or profiled entrance for ions entering the ion funnel-based collision cell. An insulation material may be disposed adjacent to or in contact with each entrance member of the at least one pair of the adjacently disposed entrance members to prevent, outside of each successively larger opening, flow of gas between each entrance member of the at least one pair of the adjacently disposed entrance members.