Abstract: In various aspects, ion sources, mass spectrometer systems, and a power supply circuit coupled to a feedback circuit are provided. A power supply is provided that includes at least the power supply circuit and is operable to transfer charge to a load. The feedback circuit is responsive to a DC component of an output voltage supplied by the power supply in a first feedback loop and an AC component of the output voltage in a second feedback loop to produce a feedback signal representative of at least one of: a value of the output voltage before a charge transfer from a capacitor of the power supply to a load; the value of the output voltage during the charge transfer from the capacitor of the power supply to the load; or the value of the output voltage after the charge transfer from the capacitor of the power supply to the load.

Abstract: Systems and methods for analyzing compounds in a sample. In one embodiment, the present technology is directed towards a method of analyzing a sample, comprising: emitting ions from the sample; selectively filtering the emitted ions for at least one designated trigger ion; fragmenting the designated trigger ions; scanning for a designated trigger ion fragment; and upon detecting the designated trigger ion fragment, scanning for at least one confirmatory ion fragment.

Abstract: Systems and methods for analyzing compounds in a sample. In one embodiment, a mass spectrometer includes an ion source for emitting a plurality of ions from a sample together with a detector positioned downstream of said ion source and configured to detect the impact of emitted ions on the detector. The mass spectrometer also includes a controller operatively coupled to the detector and to the ion source and configured to calculate the m/z for each detected ion. The controller comprises a mass defect filter configured to determine if the m/z for each detected ion falls within a pre-determined mass defect range. The mass spectrometer also includes data storage coupled to the controller, wherein the data storage is configured to store detected ion m/z data corresponding to the m/z for a detected ion if the m/z falls within the mass defect range. The mass spectrometer may also include an ion mass filter positioned downstream of the ion source and operatively coupled to the controller.

Abstract: According to various embodiments, variables are grouped in an unsupervised manner after principal component analysis of a plurality of variables from a plurality of samples. A number of principal components are selected. A subset principal component space is created for those components. A starting variable is selected. A spatial angle is defined around a vector extending from the origin to the starting variable. A set of one or more variables is selected within the spatial angle. The set is assigned to a group. The set is removed from further analysis. The process is repeated starting with the selection of a new starting variable until all groups are found.

Abstract: A mass spectrometer system having an ion trap and a downstream mass spectrometer is provided. A plurality of groups of ions are provided to the ion trap and a first mass-to-charge ratio is selected. The downstream mass spectrometer is configured to filter out one of (i) ions having a first unselected mass-to-charge ratio different from the first mass-to-charge ratio, and (ii) mass signals for ions having the first unselected mass-to-charge ratio different from the first mass-to-charge ratio. A first group of ions is ejected of the first mass-to-charge ratio from the ion trap to the downstream mass spectrometer.

Abstract: Methods for fragmenting ions retained in an ion trap are described. In various embodiments, a non-steady-state pressure of a neutral collision gas of less than about 5×10?4 Torr and an excitation amplitude of less than about 500 mV (peak to ground) is used to fragment ions with greater than about 80% fragmentation efficiency. In various embodiments, duration of ion excitation is greater than about 25 ms.

Abstract: Methods for fragmenting ions in an ion trap are described.

Abstract: A method of operating an ion trap spectrometer system having an ion trap is provided.

Abstract: In a tandem mass spectrometer using a collision cell for ion fragmentation, the upper limit of the collision energy required for collision induced dissociation (CID) can be extended without reaching or going beyond the upper electrical discharge limit of the system components. The present teachings describe a method of lifting the potential energy of ions to a predetermined level sufficient for CID fragmentation while satisfying a discharge free condition. The present teaching also describes a method of lifting the potential energy of the fragment ions after CID fragmentation so that the product ions have sufficient energy for mass analysis.

Abstract: The applicants' teachings provide methods, systems, and apparatus useful in operating mass spectrometers and other devices incorporating multipole rod sets or other multi-electrode devices to simultaneously contain ions of both positive and negative charges through the simultaneous application to the rods or other electrodes of both radio-frequency (RF) and alternating (AC) currents.

Abstract: Ion trap apparatus and methods for efficiently addressing the effects of charge space caused by ion trap overfilling, useful in linear ion traps of mass spectrometers.

Abstract: In various embodiments the present teachings provide high-voltage, asymmetric-waveform power supplies useful for, e.g., differential mobility spectrometry. In various embodiments, provided are high-voltage, asymmetric-waveform power supplies for high-field asymmetric waveform ion mass spectrometers having field values greater than about 5,000 volts cm?1 and varying in time at rates greater than about 600 kilohertz (KHz).

Abstract: Systems, methods, and computer program products useful in controlling the fragmentation of ions. Control of fragmentation is achieved by varying the collision energy imparted to precursor ions.

Abstract: A mass spectrometer and a method of operating and building same is provided in which a hexapole component is deliberately added to a substantially quadrupole field. This can result in unwanted octopole and dipole fields also being added to the substantially quadrupole field. Modifications to the mass spectrometer as well as ways of operating the mass spectrometer are provided for dealing with the unwanted octopole and dipole fields.

Abstract: Methods for improved separation of ions from an ion trap employing a combination of low pressure and low amplitude ion excitation, including methods for removing, from an ion trap ion population, ions having a m/z value neighboring that of an ion of interest, mass spectrometry methods providing improved resolution of ion detection, and programmable apparatus programmed with instructions therefor.

Abstract: In various aspects, the present teachings provide systems and methods for reducing chemical noise in a mass spectrometry instrument that use a neutral chemical reagent and one or more mass filters to reduce interfering chemical background ion signals that are generated by ionization sources of mass spectrometers. In various embodiments, the neutral chemical reagent belongs to the class of organic chemical species containing a disulfide functionality.

Abstract: In various embodiments, provided are ion optics systems comprising an even number of ion mirrors arranged in pairs such that a trajectory of an ion exiting the ion optics system can be provided that intersects a surface substantially parallel to an image focal surface of the ion optics system at a position that is substantially independent of the kinetic energy the ion had on entering the ion optics system. In various embodiments, provided are ion optics systems comprising an even number of ion mirrors arranged in pairs where the first member and second member of each pair are disposed on opposite sides of a first plane such that the first member of the pair has a position that is substantially mirror-symmetric about the first plane relative to the position of the second member of the pair.

Abstract: Disclosed is a method of determining when to calibrate a time-of-flight mass spectrometer. In various embodiments, the method comprises storing within a controller a set of parameters for the mass spectrometer; providing an updated set of parameters while retaining at least one set of previously stored parameters; computing at least one rate of change of the updated set of parameters with respect to the at least one set of previously stored parameters; and determining when to calibrate the mass spectrometer from the results of computing the rate of change of at least one of the parameters. In various embodiments, a parameter stored can be a set of temperatures derived from obtaining system temperature measurements of those components whose changing temperature is an indication of mass drift.

Abstract: Disclosed are methods and apparatus for compensating for mass error for a time-of-flight mass spectrometer. A reference flight distance for a pulse of ions corresponding to a reference temperature of one or more components of an ion flight path assembly is determined, and the temperature of one or more components of the ion flight path assembly is measured. Correlating the thermal expansion of the flight path assembly with the temperature measurement allows the measured flight times to be adjusted to correspond with the reference flight distance to thereby compensate for the thermal expansion of the flight path assembly. A mass spectrum is obtained using the adjusted flight times. In various embodiments, the temperature signal is used with pre-determined thermal expansion correction factors for the flight path assembly to calculate a correction factor to control another component of the TOF MS, such as the voltage applied to a power supply system or a signal to control clock frequencies.

Abstract: A method, system, kit and uses for quantifying and normalizing at least one product of ethanol metabolism are provided. A method is provided for quantifying and normalizing at least one product of ethanol metabolism in a sample comprising creatinine. The method comprises adding a predetermined amount of at least one internal standard to the sample; adding deuterated creatinine to the sample; detecting and measuring at least one product of ethanol metabolism, the predetermined amount of at least one internal standard in the sample, the deuterated creatinine, and the creatinine. The method also comprises quantifying the amount of at least one product of ethanol metabolism in the sample using the measurement of the at least one internal standard; quantifying the amount of creatinine in the sample using the measurement of the deuterated creatinine; and normalizing the quantity of the at least one product of metabolism using the measurement of the creatinine.