The present disclosure provides methods and systems for performing mass spectrometry in which at least two batches of precursor ions generated via ionization of at least two different portions of a sample are exposed to electron beams at different energies to cause fragmentation of at least a portion of the precursor ions. In some embodiments, the electron energies can be selected such at one of the electron energies, EIEIO fragmentation can occur while at the other electron energy, EIEO fragmentation channel is not available. The mass spectra corresponding to the two energies can then be utilized to generate a resultant mass spectrum in which mass peaks corresponding to ion fragments generated by EIEIO dissociation are more readily identifiable.

Mass spectrometry cells include one or more interleaved magnetostatic and electrostatic lenses. In some examples, the electrostatic lenses are based on electrical potentials applied to magnetostatic lens pole pieces. In other alternatives, the electrostatic lenses can include conductive apertures. Applied voltages can be selected to trap or transport charged particles, and photon sources, gas sources, ion sources, and electron sources can be provided for various dissociation processes.

Disclosed is a system and method of mass spectrometry, including: a. ionizing an analyte to form a precursor ion (A) having a mass-to-charge ratio (m/z), in which m represents the mass and z the electric charge number; b. activating the precursor ion (A) by interaction with a beam of neutral species, ions, electrons or photons, having an energy chosen on the basis of the physicochemical properties of the precursor ion, the activation being suitable for producing a product ion (B, C) having the same mass m as the precursor ion (A) and an electric charge number z such that z is a non-zero integer different from z; c. separating the product ion (B, C, E, F) having a predefined mass-to-charge ratio (m/z); d. detecting the product ion (B, C) having the predefined mass-to-charge ratio (m/z).

When, in performing MS/MS analysis on a multivalent ion originated from a target component, an analyzing operator inputs at least two values of a mass value m.sub.Loss of an eliminated fragment, a valence z.sub.Loss of the eliminated fragment, a valence z.sub.Prec of a precursor ion and a valence z.sub.Prod of a product ion by an inputting unit, a valence calculating unit calculates an uninput valence z.sub.Prec or z.sub.Prod based on the relation, z.sub.Prec=z.sub.Prod+z.sub.Loss. Upon the start of the MS/MS analysis, a precursor ion m/z setting unit sets m/z=M.sub.Prec of an ion that passes through a front-stage quadrupole mass filter , and a passed product ion m/z calculating unit calculates m/z=M.sub.Prod of the product ion that passes through a rear-stage quadrupole mass filter by applying M.sub.Prec, m.sub.Loss, z.sub.Prec and z.sub.Prod above to the relational expression, M.sub.Prod=(M.sub.Precz.sub.Precm.sub.Loss)/z.sub.Prod.

A method and apparatus for analyzing samples using mass spectrometry are disclosed. The apparatus includes a reaction device configured to dissociate sample ions into fragments by reacting the sample ions with a charged species (e.g., electrons) such as through ECD, EID, or EIEIO. The kinetic energy of the charged species is such that the fragments may be detected and produce spectra that allow for the determination of isomeric species in the sample and the location of double bonds of sample molecules. The fragments may include radical fragments and non-radical fragments. The apparatus may also include an oxygen gas source configured to react with the radical fragments to produce oxygen-radical fragments. Spectra resulting from analysis of the fragments may allow for the determination of the oxygen-radical fragments resulting from the dissociation of the sample molecules.

A dual-ionization mass spectrometer includes a first mass spectrometer module forming a hard ionization mass spectrometer, a second mass spectrometer forming a soft ionization mass spectrometer, a vacuum ultraviolet light source positioned between the first and second modules, a housing encompassing the first and second sets of plates and the light source, and an inlet positioned to receive a sample of an analyte and provide it to at least one of the sets of plates. A method of detecting a substance includes receiving a sample of an analyte into a housing through an inlet, performing soft ionization mass spectrometry on the sample with a soft ionization mass spectrometer in the housing, performing hard ionization spectrometry on the sample with a hard ionization spectrometer in the housing if needed, and generating a detection result from at least one of the soft ionization spectrometry and the hard ionization spectrometry.

Methods are described for measuring the amount of a vitamin B2 in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying vitamin B2 in a sample utilizing on-line extraction methods coupled with tandem mass spectrometric techniques.

Methods and systems for controlling a filament of an electron emitter associated with an ion reaction cell in accordance with various aspects of the present teachings may account for inter-filament and inter-instrument variability and can provide improved reproducibility in EAD experiments and ease of use. In some aspects, a method of operating an ion reaction device of a mass spectrometer system is provided. The method comprises applying a calibration drive voltage to a filament of an electron emitter associated with an ion reaction cell and determining a value representative of the calibration electron emission current generated by the filament while having the calibration drive voltage applied thereto. A calibration saturation voltage can be determined by iteratively increasing the calibration drive voltage applied to the filament and determining the value of the calibration electron emission current at each corresponding calibration drive voltage until the filament reaches a saturation condition.

A mass spectrometer is disclosed comprising a liquid chromatography device for separating ions. A gas phase ion-neutral reaction device is arranged downstream to perform a gas phase ion-neutral reaction such as Hydrogen-Deuterium exchange. A control system is arranged to automatically and repeatedly switch the reaction device back and forth between a first mode of operation and a second mode of operation, wherein in the first mode of operation at least some parent or precursor ions are caused to react within the reaction device and wherein in the second mode of operation substantially fewer or no parent or precursor ions are caused to react.

An ion sequestering apparatus and methods or systems using one or more auxiliary electrodes in an ion reaction instrument having RF electrodes adapted to guide positively-charged precursor ins along a first axis, and an electron source for introduction of an electron beam along a second axis transverse to the first axis such that electron activated dissociation of the precursor ions into reaction products can occur, the auxiliary electrode configured to apply a supplemental AC signal to permit selective extraction of reaction products while sequestering precursor ions along the second central axis. For example, the supplemental AC signal can comprises an notched white noise signal with a notch that suppresses frequencies at which the precursor ions (and/or charge reduced species that have the same molecular mass but have a different charge state) would otherwise be excited.