In an inductively coupled plasma-mass spectrometry (ICP-MS) system, ions are transmitted into a collision/reaction cell. A DC potential is applied at an exit of the cell at a first magnitude to generate a DC potential barrier effective to prevent the ions from exiting the cell. The DC potential barrier is maintained during a confinement period to perform an interaction. After the confinement period, analyte ions or product ions are transmitted to a mass spectrometer by switching the exit DC potential to a second magnitude effective to allow the analyte ions or product ions to pass through the cell exit as a pulse. The analyte ions or product ions are then counted during a measurement period. The interaction may be ion-molecule reactions or ion-molecule collisions.

A method of performing a computation using a quantum computer includes generating a first laser pulse and a second laser pulse to cause entanglement interaction between a first trapped ion and a second trapped ion of a plurality of trapped ions that are aligned in a first direction, each of the plurality of trapped ions having two frequency- separated states defining a qubit, and applying the generated first laser pulse to the first trapped ion and the generated second laser pulse to the second trapped ion. Generating the first laser pulse and the second laser pulse includes stabilizing the entanglement interaction between the first and second trapped ions against fluctuations in frequencies of collective motional modes of the plurality of trapped ions in a second direction that is perpendicular to the first direction.

A method for analyzing a sample includes trapping a first ion packet in a first segment of a multi-segment reaction cell; trapping a second ion packet in a second segment of the multi-segment reaction cell; and trapping a third ion packet in a third segment of the multi-segment reaction cell. At least one of the first, second, and third ion packets includes precursor ions, and at least another one of the first, second, and third ion packets includes reagent ions. The method further includes mixing the first, second, and third ion packets within the reaction cell to cause a reaction between the precursor ions and the reagent ions to form product ions.

A method is described that produces product ions for mass analysis, the method comprising the steps of: introducing precursor ions into an RF electric field ion containment device, introducing reagent ions into the RF electric field ion containment device and performing an ion-ion interaction in the RF electric field ion containment device by co-trapping the precursor ions with the reagent ions. Precursor ions and product ions may be retained and/or isolated in the RF electric field ion containment device. The steps above may be repeated until a predetermined amount of reaction completeness is attained. Mass analysis of at least some of the ions in the RF electric field ion containment device may be performed where the ions are mass analyzed either directly from the RF electric field ion containment device.

A dissociation device fragments a precursor ion, producing at least two different product ions with overlapping m/z values in the dissociation device. The dissociation device applies an AC voltage and a DC voltage creating a pseudopotential that traps ions below a threshold m/z including the at least two product ions. The dissociation device receives a charge reducing reagent that causes the trapped at least two product ions to be charge reduced until their m/z values increase above the threshold m/z set by the AC voltage. The increase in the m/z values of the at least two product ions decreases their overlap. The at least two product ions with increased m/z values are transmitted to another device for subsequent mass analysis by applying the DC voltage to the dissociation device relative to a DC voltage applied to the other device.

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.

A method and corresponding apparatus are disclosed for analysis of a peptide-containing sample. The sample is prepared by adding isotopically-labeled peptides corresponding to endogenous peptides of interest, and the prepared sample is analyzed by liquid chromatography-mass spectrometry (LCMS). Detection in a high-resolution, accurate mass (HRAM) MS1 spectrum of a precursor ion matching an isotopically-labeled peptide triggers acquisition of an MS/MS spectrum (preferably acquired in an ion trap or other fast mass analyzer) to determine if a product ion is present matching a characteristic product ion (e.g., the y.sub.1 ion) of the isotopically-labeled peptide. If the characteristic product ion is present, then a HRAM MS/MS spectrum is acquired for detection and quantitation of the corresponding endogenous peptide.

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.

A method of mass spectrometry is disclosed for determining if a mutated variant of a target protein is present in a sample. The method comprises subjecting the sample to fragmentation so as to cause said target protein to fragment to form second generation fragment ions, and then mass analysing these fragment ions to obtain spectral data. The method determines if a mutated variant is present in the sample by determining that an ion in the spectral data has a mass to charge ratio that differs from the mass to charge ratio of an ion that would be observed if said target protein was a normal unmutated version of said target protein, and by an amount that corresponds to a mass difference that would be caused by the target protein being a mutated variant of said target protein. This method of analysing second generation fragment ions if a rapid and efficiency method of analysing a sample.

A method of mass or ion mobility spectrometry is disclosed comprising: providing an ion source for generating analyte ions and reference ions; providing a mass analyzer or ion mobility separator (IMS); providing an ion trap between the ion source and the mass analyzer or IMS; guiding reference ions from the ion source into the ion trap and trapping the reference ions in the ion trap; guiding the analyte ions from the ion source into the mass analyzer or IMS, wherein the analyte ions bypass the ion trap; and releasing reference ions from the ion trap into the mass analyzer or IMS for analysis.