Abstract: A method of ion detection comprises: (a) setting electrical potentials of a dynode and a scintillator electrode of a Daly detector and of a focusing lens disposed at an ion inlet of the Daly detector so as to detect negatively charged ions received from a mass analyzer or mass filter; (b) transferring the negatively charged ions from the mass analyzer or mass filter to the Daly detector through the lens and detecting said negatively charged ions by a photodetector of the Daly detector; (c) setting electrical potentials of the dynode, the scintillator electrode and the focusing lens of the Daly detector so as to detect positively charged ions received from the mass analyzer or mass filter; and (d) transferring the positively charged ions from the mass analyzer or mass filter to the Daly detector through the lens and detecting said positively charged ions by the photodetector.

Abstract: 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.

Abstract: A dual polarity ion detector comprises: an entrance electrode disposed to receive ions and maintained at a reference voltage, V0; a first dynode maintained at a voltage, V1, that is negative relative to V0; a second dynode maintained at a voltage, V2, that is positive relative to V0; a shielding electrode disposed between the first and second dynodes and maintained at a voltage, V3; 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, Vaperture; that is intermediate between the voltage, V1, and the voltage, V2. In some instances, the voltage, V3, may be equal to or approximately equal to the voltage, V0.

Abstract: A mass spectrometer system comprises: (a) an ion source; (b) a mass filter or a time-of-flight (TOF) ion separator configured to receive a stream of first-generation ions from the ion source; (c) an ion storage device having an ion inlet configured to receive a stream of filtered ions comprising a plurality of ion species from the mass filter or TOF separator and to accumulate the plurality of ion species therein; (d) an ion mobility cell having an ion inlet configured to receive an accumulated batch of ion species from the ion storage device and an ion outlet configured to release, one at a time, the individual ion species therefrom; and (e) a mass analyzer configured to receive and mass analyze each first-generation ion species or each fragment ion species generated by fragmentation or other reaction of the various first-generation ion species.

Abstract: 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.

Abstract: A mass spectrometer system comprises: (a) an ion source; (b) a mass filter or a time-of-flight (TOF) ion separator configured to receive a stream of first-generation ions from the ion source; (c) an ion storage device having an ion inlet configured to receive a stream of filtered ions comprising a plurality of ion species from the mass filter or TOF separator and to accumulate the plurality of ion species therein; (d) an ion mobility cell having an ion inlet configured to receive an accumulated batch of ion species from the ion storage device and an ion outlet configured to release, one at a time, the individual ion species therefrom; and (e) a mass analyzer configured to receive and mass analyze each first-generation ion species or each fragment ion species generated by fragmentation or other reaction of the various first-generation ion species.

Abstract: Systems, methods, and devices to dissociate ions using one or more light emitting diodes (LEDs). A mass spectrometer for ion dissociation includes an ion source for providing ions for dissociation, a mass analyzer, and a photodissociation (PD) device. The PD device includes an ion transport device. The ion transport device is configured perform one or more of: transporting the ions through the PD device, and trapping the ions within a region of the PD device. The PD device also includes one or more LEDs positioned to irradiate the ions in the PD device, resulting in fragmentation of the ions.

Abstract: A system includes an optical measurement unit that measures an optical property of a whole blood sample deposited on a surface of a substrate, an ion source that causes ions derived from the whole blood sample, including ions formed from an analyte of interest present in the whole blood sample, to be emitted from the substrate, a mass analyzer that receives the ions emitted from the substrate and measures an abundance of at least one ion species corresponding to the analyte of interest, and at least one computing device that determines, based on the measured optical property, a hematocrit of the whole blood sample, and determines, based on the determined hematocrit of the whole blood sample and the measured abundance of the at least one ion species, a concentration of the analyte of interest per unit volume of blood plasma.

Abstract: A system includes an optical measurement unit that measures an optical property of a whole blood sample deposited on a surface of a substrate, an ion source that causes ions derived from the whole blood sample, including ions formed from an analyte of interest present in the whole blood sample, to be emitted from the substrate, a mass analyzer that receives the ions emitted from the substrate and measures an abundance of at least one ion species corresponding to the analyte of interest, and at least one computing device that determines, based on the measured optical property, a hematocrit of the whole blood sample, and determines, based on the determined hematocrit of the whole blood sample and the measured abundance of the at least one ion species, a concentration of the analyte of interest per unit volume of blood plasma.

Abstract: Systems, methods, and devices to dissociate ions using one or more light emitting diodes (LEDs). A mass spectrometer for ion dissociation includes an ion source for providing ions for dissociation, a mass analyzer, and a photodissociation (PD) device. The PD device includes an ion transport device. The ion transport device is configured perform one or more of: transporting the ions through the PD device, and trapping the ions within a region of the PD device. The PD device also includes one or more LEDs positioned to irradiate the ions in the PD device, resulting in fragmentation of the ions.

Abstract: A method of quantitative mass analysis of precursor ion species of different mass-to-charge (m/z) ratios from the same or common ion injection event is disclosed. A plurality of precursor ion species with different respective m/z ratios are introduced into an ion trap mass analyzer at the same time. The precursor ion species are isolated. A first subset of the isolated precursor ions, which are multiply charged and have a first m/z ratio range, is fragmented and scanned by dividing the scan into at least two separate scan windows. A first mass spectrum is generated for the fragment ions of the first subset of precursor ions. A second subset of the isolated precursor ions having a second m/z ratio is fragmented and scanned, and a second mass spectrum is generated for the fragment ions of the second subset of precursor ions.

Abstract: A mass spectrometry apparatus includes an ion source, an ion trap and a mass spectrometer controller. The ion source is configured to generating ions. The ion trap is configured to trap ions within a RF field; eject unwanted ion while retaining target ions; and fragment target ions. The mass spectrometer controller is configured to determine an injection time for the ion trap based on a precursor ion flux and a product ion flux; fill the ion trap with ions from the ion source for an amount of time equal to the injection time; isolate target precursor ions in the ion trap; fragment the target precursor ions to generate product ions; and mass analyzing the product ions.

Abstract: A method of quantitative mass analysis of precursor ion species of different mass-to-charge (m/z) ratios from the same or common ion injection event is disclosed. A plurality of precursor ion species with different respective m/z ratios are introduced into an ion trap mass analyzer at the same time. The precursor ion species are isolated. A first subset of the isolated precursor ions, which are multiply charged and have a first m/z ratio range, is fragmented and scanned by dividing the scan into at least two separate scan windows. A first mass spectrum is generated for the fragment ions of the first subset of precursor ions. A second subset of the isolated precursor ions having a second m/z ratio is fragmented and scanned, and a second mass spectrum is generated for the fragment ions of the second subset of precursor ions.

Abstract: A mass spectrometer includes a radio frequency ion trap and a controller. The controller is configured to cause an ion population to be injected into the radio frequency ion trap and supply an isolation waveform to the radio frequency ion trap. The isolation waveform has at least one notch at a target mass-to-charge ratio and a frequency profile determined to eject unwanted ions at a plurality of frequencies in a substantially similar amount of time.

Abstract: Techniques can increase the resolution and accuracy of mass spectra obtained using ion traps through the use of the actual shape of the ion trap peaks, which is a series of smaller ion ejection events. The peak shapes are identified as changing over a common period of the trapping signal and the excitation signal, at which point the peak shapes repeat. Peak shapes can be characterized over the common period to create N basis functions, each for a different fractional mass for a given scan rate. The N basis functions over the common period can be duplicated (e.g., shifted by the common period) to obtain a set of mass functions that characterize fractional masses over the full scan range. The mass spectrum can be obtained by fitting the set of mass functions to the measured data to obtain a best fit contribution of each mass function to the measured data.

Abstract: A mass spectrometer includes a radio frequency ion trap; and a controller. The controller is configured to cause an ion population to be injected into the radio frequency ion trap; supply a first isolation waveform to the radio frequency ion trap for a first duration, and supply a second isolation waveform to the radio frequency ion trap for a second duration. The first isolation waveform has at least a first wide notch at a first mass-to-charge ratio, and the second isolation waveform has at least a first narrow notch at the first mass-to-charge ratio. The first and second isolation waveforms are effective to isolate one or more precursor ions from the ion population.

Abstract: A method of aligning a light beam within a mass spectrometer includes providing precursor ions along a longitudinal axis of the mass spectrometer at two or more precursor ion locations, the precursor ion locations being spatially separated along the longitudinal axis of the mass spectrometer, the precursor ions forming in-vacuum targets. The method then includes directing a light beam from a light source in a direction along the longitudinal axis of the mass spectrometer, the light beam photo-dissociating the precursor ions, and monitoring a mass spectrometer ion signal from each of the two or more precursor ion locations while adjusting the direction of the light beam, thereby aligning the light beam within the mass spectrometer.

Abstract: Techniques can increase the resolution and accuracy of mass spectra obtained using ion traps through the use of the actual shape of the ion trap peaks, which is a series of smaller ion ejection events. The peak shapes are identified as changing over a common period of the trapping signal and the excitation signal, at which point the peak shapes repeat. Peak shapes can be characterized over the common period to create N basis functions, each for a different fractional mass for a given scan rate. The N basis functions over the common period can be duplicated (e.g., shifted by the common period) to obtain a set of mass functions that characterize fractional masses over the full scan range. The mass spectrum can be obtained by fitting the set of mass functions to the measured data to obtain a best fit contribution of each mass function to the measured data.

Abstract: A method and apparatus are disclosed for dissociation of precursor ions, such as polypeptides, by ultraviolet photodissociation (UVPD) for mass spectrometry analysis. Precursor ions are confined within an ion trap and irradiated with ultraviolet (UV) light, which may take the form of pulses emitted by a laser. The precursor ions absorb the UV light and dissociate into product ions. To avoid the condition of overfragmentation arising from further dissociation of the product ions, an excitation field is established within the ion trap such that the product ions, but not the precursor ions, are kinetically excited to trajectories that extend outside of the irradiated region.

Abstract: A mass spectrometer includes a radio frequency ion trap; and a controller. The controller is configured to cause an ion population to be injected into the radio frequency ion trap; supply a first isolation waveform to the radio frequency ion trap for a first duration, and supply a second isolation waveform to the radio frequency ion trap for a second duration. The first isolation waveform has at least a first wide notch at a first mass-to-charge ratio, and the second isolation waveform has at least a first narrow notch at the first mass-to-charge ratio. The first and second isolation waveforms are effective to isolate one or more precursor ions from the ion population.