Abstract: 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.

Abstract: One or more ions are received along a central axis through a first set of reflectron plates of an ELIT. Voltages are applied to the first set of plates and to a second set of reflectron plates in order to trap and oscillate the one or more ions. A first induced current is measured from a cylindrical pickup electrode between the first set of reflectron plates and the second set of reflectron plates. A second induced current is measured from one or more plates of the first set of reflectron plates. A third induced current is measured from one or more plates of the second set of reflectron plates. The first measured induced current, second measured induced current and third measured induced current are combined to reduce higher order frequency harmonics of the induced current.

Abstract: A back-illuminated semiconductor light detecting device includes a light detecting substrate having pixels, and a circuit substrate having signal processing units. For each of the pixels, the light detecting substrate includes avalanche photodiodes respectively having light receiving regions provided in a first main surface side of the semiconductor substrate. In the semiconductor substrate, for each pixel, a trench surrounds at least one region including the light receiving region when viewed from a direction perpendicular to the first main surface. The number of signal processing units is larger than the number of light receiving regions in each pixel, and the number of regions surrounded by the trench in each pixel is equal to or less than the number of light receiving regions in the pixel.

Abstract: A system and method is described for characterizing glycopeptides which includes a first quadrupole mass filter, a multipole rod set of an ion guide, a lens electrode, an ExD device and a mass analyzer. The multipole rod set is adapted to receive a radial radio frequency (RF) trapping voltage and a radial dipole direct current (DC) voltage The lens electrode is adapted to receive an axial trapping alternating current (AC) voltage and a DC voltage. The ExD device performs electron capture dissociation or electron transfer dissociation, the ExD device being positioned so that an entrance of the ExD device is disposed on the other side of the lens electrode opposite the multipole rod set. The mass analyzer is positioned at an exit of the ExD device for receiving ions from the ExD device.

Abstract: 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 and/or the orientation of those double bonds within the sample molecules. The fragments may include radical fragments and non-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 as confirmation of the presence of those radical fragments.

Abstract: A photodetecting device includes a semiconductor substrate, a plurality of avalanche photodiodes each having a light receiving region, the avalanche photodiodes being arranged in a matrix at the semiconductor substrate, and a plurality of through-electrodes electrically connected to corresponding light receiving regions. The plurality of through-electrodes are arranged for each area surrounded by four mutually adjacent avalanche photodiodes of the plurality of avalanche photodiodes. Each of the light receiving regions has, when viewed from a direction perpendicular to a first principal surface of the semiconductor substrate, a polygonal shape including a pair of first sides opposing each other in a row direction and extending in a column direction and four second side opposing four through-electrodes surrounding the light receiving region and extending in directions intersecting with the row direction and the column direction. The length of the first side is shorter than the length of the second side.

Abstract: A mass isolation device selects a precursor ion of a sample that has been digested using a protease. A first fragmentation device fragments the precursor ion using collision-induced dissociation (CID), and the resulting product ions are analyzed using a mass analyzer producing a CID spectrum. A list of theoretical candidate glycopeptide sequences is determined from CID spectrum. The mass isolation device again selects the precursor ion of the sample. A second fragmentation device fragments the precursor ion using electron-based dissociation (ExD), and the resulting product ions are analyzed using the mass analyzer producing a CID spectrum. For each sequence of the list, the sequence is computationally fragmented, producing theoretical fragments, mass-to-charge ratio (m/z) values are calculated for the theoretical fragments, and the sequence is scored using c and z fragment matching rules. The highest scoring sequence is identified as a peptide sequence of a glycopeptide of the sample.

Abstract: In one aspect, an ion trap is disclosed, which includes a curved linear ion trap having a plurality of electrodes arranged around a central curved axis so as to provide a volume for trapping ions, said plurality of electrodes comprising at least one inner electrode and at least one outer electrode radially separated from said inner electrode. The ion trap further includes a pair of inner and outer ion guide electrodes providing a volume therebetween for receiving ions ejected from said curved ion trap and guiding the ejected ions to one or more spatial locations along a focal line, said inner and outer ion guide electrodes being positioned external to said ion trapping volume and in proximity of said at least inner and outer electrodes of the curved ion trap, respectively, wherein a DC voltage is applied between said ion guide electrodes to provide an electric filed therebetween for guiding the ejected ions to said spatial locations.

Abstract: A separation device separates an unknown intact mAb or reduced mAb subunits of a known mAb class from a sample. M An ion source device ionizes the mAb. A mass spectrometer fragments the ionized mAb using an ECD device and mass analyzes resulting product ions using a mass analyzer, producing one or more product ion spectra. Theoretical product ion peaks are calculated for one or more constant portions of the mAb class. The theoretical product ion peaks are removed from the one or more product ion spectra, producing one or more difference product ion spectra. De novo sequencing is applied to the one or more difference product ion spectra, producing one or more candidate sequences for one or more variable portions of the mAb. A genome database is searched for matches to the one or more candidate sequences, producing one or more matched sequences for the one or more variable portions.

Abstract: A photodetecting device includes a semiconductor substrate including a first principal surface and a second principal surface that oppose each other and a plurality of through-electrodes penetrating through the semiconductor substrate in a thickness direction. The semiconductor substrate includes a plurality of avalanche photodiodes arranged to operate in Geiger mode. The plurality of through-electrodes are electrically connected to the corresponding avalanche photodiodes. The semiconductor substrate includes a first area in which the plurality of avalanche photodiodes are distributed in at least a first direction and a second area in which the plurality of through-electrodes are distributed two-dimensionally. The first area and the second area are distributed in a second direction orthogonal to a first direction when viewed from a direction orthogonal to the first principal surface.

Abstract: One or more ions are received along a central axis through a first set of reflectron plates of an ELIT. Voltages are applied to the first set of plates and to a second set of reflectron plates in order to trap and oscillate the one or more ions. A first induced current is measured from a cylindrical pickup electrode between the first set of reflectron plates and the second set of reflectron plates. A second induced current is measured from one or more plates of the first set of reflectron plates. A third induced current is measured from one or more plates of the second set of reflectron plates. The first measured induced current, second measured induced current and third measured induced current are combined to reduce higher order frequency harmonics of the induced current.

Abstract: A photodetector device includes an avalanche photodiode array substrate formed from compound semiconductor. A plurality of avalanche photodiodes arranged to operate in a Geiger mode are two-dimensionally arranged on the avalanche photodiode array substrate. A circuit substrate includes a plurality of output units which are connected to each other in parallel to form at least one channel. Each of the output units includes a passive quenching element and a capacitative element. The passive quenching element is connected in series to at least one of the plurality of avalanche photodiodes. The capacitative element is connected in series to at least one of the avalanche photodiodes and is connected in parallel to the passive quenching element.

Abstract: 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 and/or the orientation of those double bonds within the sample molecules. The fragments may include radical fragments and non-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 as confirmation of the presence of those radical fragments.

Abstract: A photodetecting device includes a semiconductor substrate, a plurality of avalanche photodiodes each including a light receiving region disposed at a first principal surface side of the semiconductor substrate, the avalanche photodiodes being arranged two-dimensionally at the semiconductor substrate, and a through-electrode electrically connected to a corresponding light receiving region. The through-electrode is provided in a through-hole penetrating through the semiconductor substrate in an area where the plurality of avalanche photodiodes are arranged two-dimensionally. At the first principal surface side of the semiconductor substrate, a groove surrounding the through-hole is formed between the through-hole and the light receiving region adjacent to the through-hole.

Abstract: A photodetecting device includes a semiconductor substrate, a plurality of avalanche photodiodes each including a light receiving region disposed at a first principal surface side of the semiconductor substrate, the avalanche photodiodes being arranged two-dimensionally at the semiconductor substrate, and a through-electrode electrically connected to a corresponding light receiving region. The through-electrode is provided in a through-hole penetrating through the semiconductor substrate in an area where the plurality of avalanche photodiodes are arranged two-dimensionally. At the first principal surface side of the semiconductor substrate, a groove surrounding the through-hole is formed between the through-hole and the light receiving region adjacent to the through-hole.

Abstract: A system and method is described for characterizing glycopeptides which includes a first quadrupole mass filter, a multipole rod set of an ion guide, a lens electrode, an ExD device and a mass analyzer. The multipole rod set is adapted to receive a radial radio frequency (RF) trapping voltage and a radial dipole direct current (DC) voltage The lens electrode is adapted to receive an axial trapping alternating current (AC) voltage and a DC voltage. The ExD device performs electron capture dissociation or electron transfer dissociation, the ExD device being positioned so that an entrance of the ExD device is disposed on the other side of the lens electrode opposite the multipole rod set. The mass analyzer is positioned at an exit of the ExD device for receiving ions from the ExD device.

Abstract: A photodetecting device includes a semiconductor substrate including a one-dimensionally distributed plurality of pixels. The photodetecting device includes, for each pixel, a plurality of avalanche photodiodes arranged to operate in Geiger mode, a plurality of quenching resistors electrically connected in series with the respective avalanche photodiodes, and a signal processing unit arranged to process output signals from the plurality of avalanche photodiodes. Light receiving regions of the plurality of avalanche photodiodes are two-dimensionally distributed for each pixel. Each signal processing unit includes a gate grounded circuit and a current mirror circuit electrically connected to the gate grounded circuit. The gate grounded circuit is electrically connected to the plurality of avalanche photodiodes of the corresponding pixel via the plurality of quenching resistors. The current minor circuit is arranged to output a signal corresponding to output signals from the plurality of avalanche photodiodes.

Abstract: Improvements to a side-on Penning trap include methods to stabilize ions in the trap. The ions are stabilized by injecting ions in the focusing region of the non-uniform DC fields produced by the pad electrodes of the trap. Ions are injected along an injection axis shifted from the central axis of a gap between a positively biased electrode pad and negatively biased electrode pad of the trap. Improvements also include methods to compensate for the Lorentz force that is produced when ions are injected into a side-on Penning trap. Electrodes of an ion injection device are DC biased so that the electrodes produce an electric field along the axis of the device that compensates for the Lorentz force. Finally, methods are provided to increase the m/z range of ions injected into a side-on Penning trap by pre-trapping ions just before injection of the ions into the trap.

Abstract: Methods and systems are provided herein for selectively removing product ions resulting from an ECD dissociation event from the interaction region of an ECD reaction cell, while other precursor peptide ions continue to undergo ECD within the interaction region, thereby reducing or preventing the occurrence of multiple electron capture events by the product ions. In some aspects, the preferential extraction of product ions from the interaction region during the ECD reaction can occur without an auxiliary AC field being generated within the interaction region. Additionally, in some aspects, the methods and systems disclosed herein can subject the various product ions to a non-dissociative charge reduction via exposure to reagent ions of the opposite polarity so as to selectively concentrate product ions to a lower charge state.

Abstract: A photodetecting device includes a semiconductor substrate, a plurality of avalanche photodiodes each including a light receiving region disposed at a first principal surface side of the semiconductor substrate, the avalanche photodiodes being arranged two-dimensionally at the semiconductor substrate, and a through-electrode electrically connected to a corresponding light receiving region. The through-electrode is provided in a through-hole penetrating through the semiconductor substrate in an area where the plurality of avalanche photodiodes are arranged two-dimensionally. At the first principal surface side of the semiconductor substrate, a groove surrounding the through-hole is formed between the through-hole and the light receiving region adjacent to the through-hole.