In one aspect, a method of calibrating a Fourier Transform (FT) multipole mass spectrometer is disclosed, which comprises measuring a plurality of secular frequencies of a calibrant ion in a multipole FT mass analyzer for a plurality of RF voltages (V.sub.RF) applied to at least one rod of the multipole mass analyzer adjusted q analyzer, calculating Mathieu β and q parameters for each of 5 the measured secular frequencies, and determining RF voltage amplitude (V.sub.RF) for each calculated q parameter. For each calculated q parameter, an offset RF voltage amplitude (ΔV.sub.RF) corresponding to a deviation of the applied V.sub.RF and the calculated V.sub.RF is determined so as to generate a ΔV.sub.RFv.s. q calibration curve.

A method and apparatus for conducting reactions between precursor ions and reagent ions, for example, a reaction between a precursor cation and an electron, such as ECD, are disclosed. The apparatus comprises first, second, and third pathways, each of which extends at least partially along a central axis, and wherein the second central axis is orthogonal to the first and third central axes. Charged species can be introduced into the second pathway as the ions are transmitted therethrough, thereby increasing precursor ion and charged species interaction without simultaneous trapping of the species.

The invention relates to a mass spectrometer, comprising an ion guide having a plurality of electrodes that are supplied with a radio frequency voltage to facilitate radial confinement of ions in an internal volume defined by inward facing surfaces of the electrodes, the internal volume including a first section having a variable radial diameter along a longitudinal axis of the ion guide, in which the electrodes are helically wound, and an adjacent second section having a substantially constant radial diameter along the longitudinal axis, wherein the electrodes extend from the first section to the second section continuously. The continuous nature of the ion guide electrodes facilitates in particular unhindered axial propagation of ions through the assembly and prevents ion losses during their transmission through different compartments of the mass spectrometer.

A sample is ionized using an ion source and the ion beam is received using a tandem mass spectrometer. An m/z range is divided into two or more precursor ion isolation windows. Two or more values for a fragmentation parameter are selected. A first value of the two or more values for the fragmentation parameter has a level that fragments a minimal amount of ions of the ion beam. The one or more additional values have increasingly aggressive levels that produce increasingly more fragmentation of the ions of the ion beam. For each precursor ion isolation window, the tandem mass spectrometer is instructed to perform a selection and fragmentation of the ion beam using the precursor ion isolation window and the first value and is instructed to perform one or more additional selections and fragmentations of the ion beam using the precursor ion isolation window and using the one or more additional values.

In one aspect, a mass spectrometer is disclosed, which comprises a Fourier Transform (FT) mass analyzer having an input port for receiving ions and an exit port through which the ions exit the FT mass analyzer, a detector disposed downstream of said FT analyzer for detecting ions exiting the FT analyzer, and a multi-segment ion guide having a plurality of segments, said multi-segment ion guide being disposed upstream of said FT mass analyzer and having an input port for receiving ions and an output port through which ions exit the FT mass analyzer. The segments of the ion guide are configured to be independently activated via application of a DC offset voltage thereto so as to adjust a length through which ions passing through the ion guide experience collisional cooling.

The present invention addresses ways to facilitate the detection and analysis of ion abundance, in particular for analysis of elemental ions, and in particular embodiments for isotope ratio analysis, by use of collision cells that employ an axial drag field, i.e. an axial electric field that exerts a drag force on ions within the cell. By means of the invention, the drag field allows an increase in the transmission in the case of Li from a few % up to almost 100%. The drag field is generated by electric fields and can be switched on and off within microsecond (μs) timescales and thus improves the sensitivity for the lighter elements dramatically. The invention allows use of collision cells for analysis of elemental ions in a simple and fast workflow with high throughput and without compromising transmission.

A coupling for connecting together vacuum-based analytical systems requiring to be vibrationally isolated, comprising: a tubular connector having a longitudinal axis, the connector comprising a first end for connection to a first analytical system and a flexible portion reducing transmission of vibrations and permitting displacement of the first analytical system in a direction transverse to the longitudinal axis of the connector; and a seal longitudinally separated from the flexible portion, for vacuum sealing between the connector and a second analytical system; wherein the connector contains ion optics for transmitting ions between the first and second analytical systems.

An electron-ion interaction module for use in a mass spectrometer, having a plurality of rod sets arranged relative to one another such that said rod sets share a common longitudinal axis and each of said rod sets is longitudinally separated from an adjacent rod set by a gap, each of said rod sets comprising a plurality of rods arranged around said common longitudinal axis. The module further includes at least one magnet disposed around said rod sets so as to at least partially surround one or more of said plurality of rod sets and configured to generate a static magnetic field along said longitudinal axis. The rod sets are configured to receive electrons from an electron source and ions from an ion source within an interaction volume defined by the rods. One or more RF voltage sources coupled to the plurality of rod sets applies voltages to the rods.

The present mass spectrometer has one or more intermediate vacuum chambers between an ion source to generate ions derived from a sample component in an atmospheric pressure atmosphere and a vacuum chamber where a mass separator is arranged, including an ion transport unit to have an ion outlet in a first intermediate vacuum chamber at a subsequent stage of the ion source and send ions to the first chamber, an exhaust opening portion to evacuate the first chamber, which is provided in front of ion flow discharged from the ion outlet into the first chamber, an ion delivery opening portion to send ions to a next stage, which is provided on a line intersecting a straight line connecting the ion outlet and the exhaust opening portion, and an ion guide to guide ions to the ion delivery opening portion by an action of a radio-frequency electric field.

A mass spectrometer is disclosed comprising an ion optics device housing having one or more external electrical connectors (1719) provided thereon. An ion optics device (301) is arranged inside the ion optics device housing, the ion optics device (301) comprising one or more electrodes for manipulating ions, the one or more electrodes being electrically connected to the one or more external electrical connectors (1719) provided on the ion optics device housing. A voltage supply housing (1717) is provided having one or more external electrical connectors provided thereon. One or more voltage supplies are arranged inside the voltage supply housing (1717), the one or more voltage supplies being in electrical communication with the one or more external electrical connectors provided on the voltage supply housing. The one or more external electrical connectors provided on the voltage supply housing are directly physically and electrically connected to the one or more external electrical connectors (1719) provided on the ion optics device housing.