The present invention is concerned with a device for charged particle transportation and manipulation. Embodiments provide a capability of combining positively and negatively charged particles in a single transported packet. Embodiments contain an aggregate of electrodes arranged to form a channel for transportation of charged particles, as well as a source of power supply that provides supply voltage to be applied to the electrodes, the voltage to ensure creation, inside the said channel, of a non-uniform high-frequency electric field, the pseudopotential of which field has one or more local extrema along the length of the channel used for charged particle transportation, at least, within a certain interval of time, whereas, at least one of the said extrema of the pseudopotential is transposed with time, at least within a certain interval of time, at least within a part of the length of the channel used for charged particle transportation.

A mass spectrometer is disclosed wherein highly charged fragment ions resulting from Electron Transfer Dissociation fragmentation of parent ions are reduced in charge state within a Proton Transfer Reaction cell by reacting the fragment ions with a neutral superbase reagent gas such as Octahydropyrimidolazepine.

An ion detector includes: a first electron multiplier for detecting first ions having a first polarity; a second electron multiplier for detecting second ions having a second polarity different from the first polarity; a first anode for capturing electrons emitted from the first electron multiplier; a second anode for capturing electrons emitted from the second electron multiplier; and a switching circuit including a first input terminal electrically connected to the first anode, a second input terminal electrically connected to the second anode, and an output terminal, the switching circuit selectively connecting one of the first input terminal and the second input terminal to the output terminal.

A method for determining in a sample, by mass spectrometry, the amount of one or more analytes selected from the group consisting of 12,13-DiHOME, 3-hydroxybutyrate (BHBA), 3-hydroxyoctanoate, 3-methylglutarylcarnitine, 3-ureidopropionate, 7-alpha-hydroxy-4-cholesten-3-one (7-Hoca), citrate, fucose, fumarate, gamma-tocopherol, glutamate, glutarate, glycerol, glycochenodeoxycholate, glycocholate, hypoxanthine, maleate, malonate, mannose, orotate, 2,3-pyrdinedicarboxylate, ribose, serine, taurine, taurochenodeoxycholate, taurocholate, palmitoleate, linolenate, xanthine, xylitol, and combinations thereof is described. The method comprises subjecting the sample to an ionization source under conditions suitable to produce one or more ions detectable by mass spectrometry from each of the one or more analytes; measuring, by mass spectrometry, the amount of the one or more ions from each of the one or more analytes; and using the measured amount to determine the amount of each of the one or more analytes in the sample.

The disclosure features mass spectrometry systems and methods that include an ion source, an ion trap, a detector subsystem featuring first and second detector elements, and a controller electrically connected to the ion source, the ion trap, and the detector subsystem and configured so that during operation of the system, the controller: applies an electrical signal to the ion source to generate positively and negatively charged particles from sample particles in the system; applies an electrical signal to the ion trap to eject a plurality of particles from the ion trap through a common aperture of the ion trap, and determines information about the sample particles based on first and second electrical signals generated by the ejected particles.

A dual polarity ion detector comprises: an entrance electrode disposed to receive ions and maintained at a reference voltage, V.sub.0; a first dynode maintained at a voltage, V.sub.1, that is negative relative to V.sub.0; a second dynode maintained at a voltage, V.sub.2, that is positive relative to V.sub.0; a shielding electrode disposed between the first and second dynodes and maintained at a voltage, V.sub.3; and an ion detector comprising an entrance aperture configured to receive first secondary particles from the first dynode and second secondary particles from the second dynode, the entrance aperture maintained at a voltage, V.sub.aperture; that is intermediate between the voltage, V.sub.1, and the voltage, V.sub.2. In some instances, the voltage, V.sub.3, may be equal to or approximately equal to the voltage, V.sub.0.

An ion detector that can detect either positive or negative ions comprises: an ion inlet comprising an ion focusing lens; a dynode having a surface configured to intercept, within a zone of interception, a stream of ions passing through the ion focusing lens, wherein a plane that is tangent to the dynode surface at the zone of interception is disposed at an angle to a line that passes through the center of the dynode surface and the center of the focusing lens; a scintillator having a surface that is configured to receive secondary electrons emitted from the zone of interception; a scintillator electrode affixed to the scintillator surface; a photodetector configured to receive photons emitted by the scintillator and to generate an electric signal in response thereto; and one or more power supplies electrically coupled to the focusing lens, the dynode, the scintillator electrode and the photodetector.

A mass spectrometer ion reaction device, useful for performing ion-ion reactions (eg. ETD, PTR) is described. The device includes a plurality of non-linear rods, that form a pair of quadrupole rod sets. The device includes an axial passageway, that allows injections of ions of both polarities into the device, and a three dimensional trapping region. Anions and cations that are injected into the device are spatially separated into different trapping regions by a DC dipole electric field generated by a DC voltage source. The device also includes a plurality of lenses to confine, transmit or receive ions in/from the device.

In a mass spectrometer according to the present invention, when MRM measurements for a plurality of MRM transitions need to be performed within one cycle, a measurement order rearranger determines an analysis sequence by sorting the measurement in ascending order of the absolute value of an optimum application voltage (an application voltage which gives the highest ionization efficiency) to the nozzle of the ESI probe. An analysis controller performs the analysis by controlling the high-voltage power source and other relevant units according to the determined analysis sequence. Since the voltage applied to the nozzle within one cycle has no period in which the voltage is changed in the decreasing direction with the same polarity, the cycle time becomes shorter than in a conventional device.

Mass spectrometry instruments are provided that are configured to provide dynamic switching between positive and negative ion preparation and analysis during a single sample analysis. Mass spectrometry analysis methods are also provided that can include switching between positive and negative ion preparation and analysis during a single sample analysis.