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.

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.

A method of performing simultaneous entangling gate operations in a trapped-ion quantum computer includes selecting a gate duration value and a detuning frequency of pulses to be individually applied to a plurality of participating ions in a chain of trapped ions to simultaneously entangle a plurality of pairs of ions among the plurality of participating ions by one or more predetermined values of entanglement interaction, determining amplitudes of the pulses, based on the selected gate duration value, the selected detuning frequency, and the frequencies of the motional modes of the chain of trapped ions, generating the pulses having the determined amplitudes, and applying the generated pulses to the plurality of participating ions for the selected gate duration value. Each of the trapped ions in the chain has two frequency-separated states defining a qubit, and motional modes of the chain of trapped ions each have a distinct frequency.

A method of performing a computation using a quantum computer includes generating a plurality of laser pulses used to be individually applied to each of a plurality of trapped ions that are aligned in a first direction, each of the trapped ions having two frequency-separated states defining a qubit, and applying the generated plurality of laser pulses to the plurality of trapped ions to perform simultaneous pair-wise entangling gate operations on the plurality of trapped ions. Generating the plurality of laser pulses includes adjusting an amplitude value and a detuning frequency value of each of the plurality of laser pulses based on values of pair-wise entanglement interaction in the plurality of trapped ions that is to be caused by the plurality of laser pulses.

An ion source is provided comprising a nebuliser or electrospray probe (1) for nebulising a sample and an impact surface or target electrode (5). The impact surface or target electrode (5) comprises a tarnishable or oxidisable metal or an alloy comprising a tarnishable or oxidisable metal. Also provided is an ion source comprising a nebuliser or electrospray probe with a central wire comprising a tarnishable or oxidisable metal or an alloy comprising a tarnishable or oxidisable metal or an alloy comprising a tarnishable or oxidisable metal. Adducts with relatively heavy metals result in simplified multiply-charged mass spectra that are easier to interpret.

The present disclosure relates to novel and improved methods of analyzing proteins, peptides and polypeptides by mass spectrometry using ion-ion reactions. More specifically the disclosure relates to improved methods for implementing the m/z selective arresting of ion-ion reactions within the ion-ion reaction cell of a mass spectrometer system during a period where ion-ion reactions are performed.

Pole electrodes (150) are disclosed for use in an ion reaction apparatus, e.g., an electron induced dissociation cell, to reduce fouling due to polymer build-up and increase the useful lifetime of such electrodes. To reduce fouling, the novel pole electrode designs include a X-shaped aperture (160) in lieu of the conventional central circular aperture. The pole electrodes are particularly useful in systems having a plurality of branched electrodes (152) defining a first axis for controlled passage of charged ions and a transverse axis for passage of an electron beam. The pole electrodes are adapted for disposition between an electron source and the branched electrodes to provide an aperture for passage of an electron beam while also impeding escape of ions and reaction products from the apparatus. The X-shaped aperture eliminates or reduces the portion of the pole electrode surface that is most prone to fouling by polymeric build-up.

Real-time search (RTS) for mass spectrometry is described. In one instance, precursor ions generated from a sample are introduced into a mass spectrometer during an introduction period. The precursor ions are fragmented to form product ions, and a mass spectrum is acquired. During the introduction period, scores indicating the similarity between the mass spectrum and a candidate mass spectrum are identified. Based on the distribution of the scores, an action is performed.

A mass spectrometer includes a controller operable to: transfer first ions of a first charge into an ion trap; apply an RF pseudopotential that radially confines the first ions in an elongate ion channel of the trap; generate a first potential well that confines the first ions within a first volume; after a specified pre-cooling time, transfer second ions of a second, opposite charge into the trap; apply one or more additional DC potentials that generate a second potential well that confines the second ions within a second volume, the first potential well being within the second potential well; cause, after cooling the second ions, the first ions and the second ions to interact and generate product ions; and generate at least one third potential well that confines the product ions, that is adjacent to the second potential well and that has a same polarity as the first potential well.

Before a sample is introduced into a liquid sample delivery device, an ion source device receives aqueous mobile phase solution from the liquid sample delivery device and ionizes compounds of the aqueous mobile phase solution, producing an ion beam. A tandem mass spectrometer performs a first neutral loss scan of the ion beam with a first neutral loss value set to a molecular weight of a first known solvent, producing a first intensity, and performs a second neutral loss scan of the ion beam with a second neutral loss value set to a molecular weight of a second known solvent, producing a second intensity. A ratio of the first intensity to the second intensity is calculated. It is determined if the aqueous mobile phase solution is properly being delivered by the liquid sample delivery device based on the ratio.