Abstract: An ion transport apparatus for a mass- or ion-mobility-spectrometer comprises: (a) a plurality of strip electrodes in a series on a fiat substrate; (b) an ion outlet aperture in the substrate disposed adjacent to a first one of the plurality of strip electrodes; (c) a cage electrode at least partially enclosing the plurality of strip electrodes and the ion outlet aperture; (d) a radio frequency (RF) voltage generator operable to supply an RF phase difference between each pair of adjacent electrodes; and (e) at least one DC voltage source operable to supply first and second DC voltages to the cage electrode and an extraction electrode and to supply respective DC bias voltages to each of the plurality of electrodes, wherein electrode strip widths of a series of the plurality of electrodes progressively increase away from the first one of the plurality of electrodes.

Abstract: The invention provides a two-dimensional ion trap, comprising a plurality of elongate electrodes positioned between first and second end electrodes, the plurality of electrodes and first and second end electrodes defining a trapping volume. A controller in electrical communication with the plurality of elongate electrodes and the first and second end electrodes is configured to progressively vary a periodic voltage applied to at least one of the plurality of elongate electrodes to cause ions to be radially ejected from the ion trap in order of their mass to charge ratios. Concurrently, the controller is configured to progressively vary a DC offset of least one of the first and second end electrodes with respect to the plurality of elongate electrodes.

Abstract: The present invention pertains to a method and apparatus which increases the efficiency with which ions are transported from a first ion trap to a second ion trap, and subsequently trapped in the second ion trap. In one aspect the invention, increased efficiency takes the form or enabling ions of both high and low mass to charge ratios to be trapped in the second ion trap at substantially the same time, or at least within a relatively small window of time. This can be achieved by minimizing the undesirable time-of-flight separation by the high and low mass to charge ratio ions as they are transported from a first ion trap to the second ion trap. This minimization can be realized by adjusting the potential energy applied to ion transfer optics disposed between the two ion traps.

Abstract: A method and apparatus involve: performing a plurality of analytical scans during normal operation of a mass spectrometer having a detection section, wherein data is generated during the analytical scans in a manner that includes use of the detection section; and automatically evaluating the data from the analytical scans to monitor whether an actual gain of the detection section changes over time.

Abstract: A method of obtaining and analyzing a mass spectrum of a sample comprising components is characterized by: setting values of a first energy level and a second energy level; chromatographically separating the components; ionizing a portion of the separated components to create precursor ions; introducing a first portion of the precursor ions into a collision or reaction cell and generating a first sub-population of ions corresponding to the first energy level; introducing a second portion of the precursor ions into the cell and generating a second sub-population of ions corresponding to the second energy level; transferring a mixture of the first and second sub-populations of ions into a mass analyzer; producing an analysis of the ions of the mixture; varying the value of at least one of the first and the second energy levels according to a pre-determined cyclical variation; repeating various above steps; and analyzing the time-variation of the analyses.

Abstract: A method and apparatus involve: performing a plurality of analytical scans during normal operation of a mass spectrometer having a detection section, wherein data is generated during the analytical scans in a manner that includes use of the detection section; and automatically evaluating the data from the analytical scans to monitor whether an actual gain of the detection section changes over time.

Abstract: A multi-resolution mass spectrometer system and intra-scanning method is introduced to enhance the measured peak resolution at different regions of a given mass spectrum while not significantly increasing the total duration of the scan. Such an arrangement enables extra resolution where necessary, such as, for example, when incorporating a slower scan rate only over a predetermined narrow low mass marker region of a given mass spectrum. Once past the marker region, the scan rate can be increased to provide the appropriate resolution for peptide identification.

Abstract: A mass spectrometer data dependent method and apparatus is introduced to alter scanning parameters based upon data acquired during that scan. Such a method an apparatus may include the identification of ion species of interest meeting user specified criteria so that a determination can be made as to whether or not the present scan is to be continued, terminated, or alternatively paused while such a decision is being made. Such a method of operation saves overall cycle time and allows examination of, for example, marker ion ratios for additional peptides that might otherwise be missed.

Abstract: An ion gate apparatus for controlling the transmission of ion pulses between an origin and a destination in a mass spectrometer is disclosed, comprising: a first split gate having a length L1, comprising a first electrode portion; and a second electrode portion electrically insulated from the first electrode portion and separated from the first electrode portion so as to form a first aperture therebetween; a second split gate disposed adjacent to the first split gate at a distance d from the first split gate and having a length L2, comprising a third electrode portion; and a fourth electrode portion electrically insulated from the third electrode portion and separated from the third electrode portion so as to form a second aperture therebetween; a first voltage source electrically connected to said first electrode portion and to said second electrode portion; a second voltage source electrically connected to said third electrode portion and to said fourth electrode portion; and a controller electrically conne

Abstract: A method of processing Fourier Transform Mass Spectrometry (FTMS) data includes performing a Fourier Transform of a part of a time domain transient and identifying from that transformed data signal peaks representative of the presence of ions. After peak identification, the full transient is then transformed, and the peaks identified in the partial transient transform are used to locate true peaks in the transformed full transient. The number of ‘false’ peaks resulting from random noise has been found to correlate to the resolution, so that using a partial transient to identify true peaks reduces the risk of false peaks being included; nevertheless this information can then be applied to the full data set when transformed. As an alternative, different parts of the full data set can be transformed and then correlated; because any noise will be random, false peaks should occur at different places in the two partial transforms.

Abstract: A method of analyzing data from a mass spectrometer provides data-dependent acquisition. An extracted ion chromatogram (XIC) is created for each m/z data point of mass spectral scans and the XIC for each m/z data point are correlated to a model function to obtain a XIC correlation value. A weighting function is applied to the XIC correlation value to obtain a current weighted intensity for each m/z point, which is used to reconstruct a weighted mass spectrum. The value or range of intensities of interest of the weighted intensity data or raw data is transformed from the time domain into the frequency domain, and the transformed data is used to make a real-time decision for the data-dependent acquisition. The data-dependent acquisition can be the performance of tandem mass spectrometry. A sample processing apparatus receives the sample and a computer readable medium provides instructions to the apparatus.

Abstract: A method and apparatus of combining two independent multipoles in an interlaced fashion to form a resultant multipole structure is introduced. Such an arrangement enables ions from two separate sources to be merged along a predetermined longitudinal direction but also enables in the reverse path, predetermined portions of ions from a single source to be directed along one or more ion channel paths to also enable, for example, simultaneous collection by a Time of Flight (TOF) mass analyzer and an ion trap.

Abstract: A technique for mass spectrometry includes: receiving first time domain data generated from a chromatographic output, the first time domain data including mass spectra; extracting second time domain data from the first time domain data, the second time domain data corresponding to a selected range of mass-to-charge ratios; transforming the second time domain data into frequency domain data; and identifying, as a function of the frequency domain data, an elution peak for a mass-to-charge ratio within the selected range. Material from the chromatographic output may thereafter be processed as a function of the identified elution peak.

Abstract: A device for improved transportation and focusing of ions in a low vacuum or atmospheric-pressure region of a mass spectrometer is constructed from one or more electro-dynamic or electrostatic focusing lenses that is/are coupled to the first electrode of a stacked ring ion guide (SRIG) to which oscillatory (e.g., radio-frequency) voltages are applied. Such configurations as disclosed herein, minimizes deleterious field effects and/or repositioning problems of desired ion transfer instruments that utilize such stacked ring ion guides by generally configuring the outlet end of the ion transfer device to a desired position within the electro-dynamic or electro-static focusing lens(es).

Abstract: A mass spectrometer data dependent method and apparatus is introduced to alter scanning parameters based upon data acquired during that scan. Such a method an apparatus may include the identification of ion species of interest meeting user specified criteria so that a determination can be made as to whether or not the present scan is to be continued, terminated, or alternatively paused while such a decision is being made. Such a method of operation saves overall cycle time and allows examination of, for example, marker ion ratios for additional peptides that might otherwise be missed.

Abstract: A multi-resolution mass spectrometer system and intra-scanning method is introduced to enhance the measured peak resolution at different regions of a given mass spectrum while not significantly increasing the total duration of the scan. Such an arrangement enables extra resolution where necessary, such as, for example, when incorporating a slower scan rate only over a predetermined narrow low mass marker region of a given mass spectrum. Once past the marker region, the scan rate can be increased to provide the appropriate resolution for peptide identification.

Abstract: A device for transporting and focusing ions in a low vacuum or atmospheric-pressure region of a mass spectrometer is constructed from a plurality of longitudinally spaced apart electrodes to which oscillatory (e.g., radio-frequency) voltages are applied. In order to create a tapered field that focuses ions to a narrow beam near the device exit, the inter-electrode spacing or the oscillatory voltage amplitude is increased in the direction of ion travel.

Abstract: A method and apparatus of combining two independent multipoles in an interlaced fashion to form a resultant multipole structure is introduced. Such an arrangement enables ions from two separate sources to be merged along a predetermined longitudinal direction but also enables in the reverse path, predetermined portions of ions from a single source to be directed along one or more ion channel paths to also enable, for example, simultaneous collection by a Time of Flight (TOF) mass analyzer and an ion trap.

Abstract: A device for improved transportation and focusing of ions in a low vacuum or atmospheric-pressure region of a mass spectrometer is constructed from one or more electro-dynamic or electrostatic focusing lenses that is/are coupled to the first electrode of a stacked ring ion guide (SRIG) to which oscillatory (e.g., radio-frequency) voltages are applied. Such configurations as disclosed herein, minimizes deleterious field effects and/or repositioning problems of desired ion transfer instruments that utilize such stacked ring ion guides by generally configuring the outlet end of the ion transfer device to a desired position within the electro-dynamic or electro-static focusing lens(es).

Abstract: An ion gate apparatus for controlling the transmission of ion pulses between an origin and a destination in a mass spectrometer is disclosed, comprising: a first split gate having a length L1, comprising a first electrode portion; and a second electrode portion electrically insulated from the first electrode portion and separated from the first electrode portion so as to form a first aperture therebetween; a second split gate disposed adjacent to the first split gate at a distance d from the first split gate and having a length L2, comprising a third electrode portion; and a fourth electrode portion electrically insulated from the third electrode portion and separated from the third electrode portion so as to form a second aperture therebetween; a first voltage source electrically connected to said first electrode portion and to said second electrode portion; a second voltage source electrically connected to said third electrode portion and to said fourth electrode portion; and a controller electrically conne