An ion trap mass spectrometer includes an ion trap including a first electrode and a second electrode different from the first electrode, a first voltage controller that periodically switches a DV voltage among DC voltages having a plurality of values and apply the DV voltages to the first electrode, and a second voltage controller that applies a sine-wave voltage to the second electrode when ions captured in the ion trap are dissociated.

The invention generally relates to systems and methods for precursor and neutral loss scan in an ion trap. In certain aspects, the invention provides a system that includes a mass spectrometer having an ion trap, and a central processing unit (CPU). The CPU includes storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to excite a precursor ion and eject a product ion in the single ion trap.

Calibration of a mass spectrometer is described. In one aspect, a mass spectrometer can generate an offset value indicative of the mass difference between the corrected and reference external calibrant ion data. By comparing the offset value to a threshold, a preliminary mass calibration can be modified, or a recalibration of the mass spectrometer is performed.

A spherical ion trap includes a substrate and an ion aperture; two RF electrodes in electrostatic communication with an ion trapping region; RF ground electrodes in electrostatic communication with the ion trapping region; and the ion trapping region bounded by opposing RF electrodes and the RF ground electrodes, such that: the ion trapping region is disposed within the ion aperture and receives ions that are selectively trapped in the ion trapping region in response to receipt of DC and RF voltages by the RF electrodes, and receipt of the DC voltages by RF ground electrodes, and the first RF electrode, the second RF electrode, the RF ground electrodes, and the ion trapping region are disposed in the same plane within the ion aperture.

A device for controlling trapped ions includes a first substrate. A second substrate is disposed over the first substrate. One or a plurality of first level ion traps is configured to trap ions in a space between the first substrate and the second substrate. One or a plurality of second level ion traps is configured to trap ions in a space above the second substrate. An opening in the second substrate is provided through which ions can be transferred between a first level ion trap and a second level ion trap.

A miniature electrode apparatus is disclosed for trapping charged particles, the apparatus including, along a longitudinal direction: a first end cap electrode; a central electrode having an aperture; and a second end cap electrode. The aperture is elongated in the lateral plane and extends through the central electrode along the longitudinal direction and the central electrode surrounds the aperture in a lateral plane perpendicular to the longitudinal direction to define a transverse cavity for trapping charged particles.

In disclosed apparatus, a plurality of optical waveguides monolithically integrated on a surface ion trap substrate deliver light to the trapping sites. Electrical routing traces defined in one or more metallization levels deliver electrical signals to electrodes of the surface electrode ion trap. A plurality of photodetectors are integrated on the substrate and arranged to detect light from respective trapping sites.

A miniature electrode apparatus is disclosed for trapping charged particles, the apparatus includes, along a longitudinal direction, a first end cap electrode, a central electrode having an aperture, and a second end cap electrode. The aperture is elongated in the lateral plane and extends through the central electrode along the longitudinal direction and the central electrode surrounds the aperture in a lateral plane perpendicular to the longitudinal direction to define a transverse cavity for trapping charged particles. Electric fields can be applied in a y-direction of the lateral plane across one or more planes perpendicular to the longitudinal axis to translocate and/or manipulate ion trajectories.

A method for analyzing a gas by mass spectrometry includes exciting ions of the gas to be analyzed in an FT ion trap, and recording a first frequency spectrum in a first measurement time interval during or after the excitation of the ions. The first frequency spectrum contains ion frequencies of the excited ions and interference frequencies. The method also includes recording a second frequency spectrum in a second measurement time interval. The second frequency spectrum contains the interference frequencies, but not the ion frequencies of the first frequency spectrum. The method further includes comparing the first frequency spectrum with the second frequency spectrum to identify the interference frequencies in the first frequency spectrum. The disclosure also relates to a mass spectrometer which is suitable for carrying out the method for analyzing the gas by mass spectrometry.

After a precursor ion has been captured within an ion trap (2), electrons having a high energy equal to or higher than 30 eV are introduced from an electron irradiator (7) into the ion trap (2) to increase the number of charges of the ion through an interaction between the electrons and the ion. Hydrogen radicals are subsequently introduced from a hydrogen radical irradiator (5) into the ion trap (2) to dissociate the ion by a hydrogen-attachment dissociation (HAD) method. The larger the number of charges of the ion is, the higher the dissociation efficiency by the HAD method becomes. Therefore, for example, even in the case of using an ion source in which most of the generated ions are singly charged ions as in a MALDI ion source, the dissociation efficiency can be improved by increasing the number of charges of the precursor ion within the ion trap (2).