Abstract: The present teachings relate to a method of filtering mass spectrometer data using a variable filter window. The width of the window can depend on the mass itself and the mass defects for a family of compounds. The teachings can be used with a plurality of compounds including but not limited to peptides and can be utilized on a brood range of mass spectrometers.

Abstract: Provided are ion sources, methods of forming ions and mass analyzer systems. In various embodiments, the present teachings provide ion sources, methods for focusing ions from an ion source, and methods for operating a time-of-flight mass analyzer. In various embodiments, the present teachings relate to matrix-assisted laser desorption/ionization (MALDI) ion sources and methods of MALDI ion source operation, for use with mass analyzers. In various aspects, provided are ion sources and methods of operation thereof that facilitate increasing one or more of sensitivity and resolution of a TOF mass analyzer configured for multiple modes of operation.

Abstract: A system and method of analyzing a sample is described. The system includes an ion source and a deflector for producing a plurality of ion beams each of which is detected in distinct detection regions. A detection system uses the information obtained from the detection region to analyze the sample.

Abstract: Sol-gel derived monolithic silica columns containing entrapped dihydrofolate reductase were used for frontal affinity chromatography of small molecule mixtures. The output from the column combined with a second stream containing the matrix molecule (HCCA) and was directly deposited onto a conventional MALDI plate that moved relative to the column via a computer controlled x-y stage, creating a semi-permanent record of the FAC run. The use of MALDI MS allowed for a decoupling of the FAC and MS methods allowing significantly higher ionic strength buffers to be used for FAC studies, which allowed for better retention of protein activity over multiple runs.

Abstract: In various embodiments, provided are methods for focusing ions for an ion fragmentor, and methods for operating an ion optics assembly. In various embodiments, the present teachings provide methods that substantially maintain the position of the focal point of the an incoming ion beam over a wide range of collision energies, and thereby provide a collimated ion beam for a collision cell over a wide range of energies. In various embodiments, the present teachings provide methods that facilitate decreasing ion transmission losses over a wide range of collision energies.

Abstract: A method and apparatus are provided for effecting multiple mass selection or analysis steps. Fundamentally, the technique is based on moving ions in different directions through separate components of a mass spectrometer apparatus. To effect different steps, a precursor ion is selected in a first mass selector, and then passed into a collision cell, to effect fragmentation or reaction with a gas, to generate fragment or product ions. The generated product ions are then passed back into the first mass selector, and preferably back into an upstream ion trap. The product ions then pass through the first mass selector again, to select a desired product ion, for further fragmentation and analysis. These steps can be repeated a number of times. A final mass analysis step can be effected in either a time-of-flight section or other mass analyzer. The invention enables conventional triple quadrupole mass spectrometers and QqTOF mass spectrometers to effect multiple MS steps.

Abstract: A method and apparatus for manipulating ions using a two-dimensional substantially quadrupole field, and a method of manufacturing and operating an apparatus for manipulating ions using a two-dimensional substantially quadrupole field are described. The field has a quadrupole harmonic with amplitude A2 and a hexapole harmonic with amplitude A3. The amplitude A3 of the hexapole component of the field is selected to improve the performance of the field with respect to ion selection and ion fragmentation.

Abstract: Improved methods for the detection and quantitation of labeled biological materials in a sample using elemental spectroscopic detection are described. Element-labeled biologically active materials, comprising antibodies, antigens, growth factors, hormones, receptors and other biologically active materials covalently attached to a stable elemental tag, can be used in specific binding assays and measured by elemental spectroscopic detection. Also described are methods for the determination of metals in samples of interest using specific antibodies to isolate the target metals and elemental spectroscopy for detection and quantitation.

Abstract: A system and method of analyzing a sample is described. The system includes an ion source and a deflector for producing a plurality of ion beams each of which is detected in distinct detection regions. A detection system uses the information obtained from the detection region to analyze the sample.

Abstract: Provided are MALDI ion sources, methods of forming ions and mass analyzer systems. In various embodiments, provided are MALDI ion sources configured to irradiate a sample on a sample surface with a pulse of laser energy at angle within 10 degrees or less of the surface normal, and a first ion optics system configured to extract sample ions in a direction within 5 degrees or less of the surface normal. In various embodiments, MALDI ion sources having substantially coaxial sample irradiation and ion extraction are provided. In various embodiments, methods are provided, which produce sample ions by MALDI and extract sample ions using an accelerating electrical field to form an ion beam, such that, the angle of the trajectory at the exit from the accelerating electrical field of sample ions substantially at the center of the ion beam is substantially independent of sample ion mass.

Abstract: Provided are ion sources, methods of forming ions and mass analyzer systems. In various embodiments, the present teachings provide ion sources, methods for focusing ions from an ion source, and methods for operating a time-of-flight mass analyzer. In various embodiments, the present teachings relate to matrix-assisted laser desorption/ionization (MALDI) ion sources and methods of MALDI ion source operation, for use with mass analyzers. In various aspects, provided are ion sources and methods of operation thereof that facilitate increasing one or more of sensitivity and resolution of a TOF mass analyzer configured for multiple modes of operation.

Abstract: A method and apparatus is disclosed to prepare a sample or a plurality of samples for subsequent analysis. A single sample deposition apparatus, and a multiplexed sample deposition apparatus are shown. The apparatus allows for a system that can provide a high throughput deposition of samples to form chromatograms by discrete droplet deposition or as continuous traces. The system can achieve high resolution digitization by pulsing the fluid emanating from the chromatographs by applying a voltage to the target plate that operates at frequencies equal to or greater than about 10 Hz, and up to and including about 1 KHz. The system also allows for analogue recording (i.e., approaching infinite resolution) by nebulizing the fluid coming from multiple columns and simultaneously collecting it on a target plate as a continuous trace.

Abstract: In a mass spectrometer, ions from an ion source pass through an inlet aperture into a vacuum chamber for transmitting prior to mass analysis by the mass analyzer. The configuration of the inlet aperture forms a sonic orifice or sonic nozzle and with a predetermined vacuum chamber pressure, a supersonic free jet expansion is created in the vacuum chamber that entrains the ions within the barrel shock and Mach disc. Once formed, at least one ion guide with a predetermined cross-section to essentially radially confine the supersonic free jet expansion can focus the ions for transmission through the vacuum chamber. This effectively improves the ion transmission between the ion source and the mass analyzer.

Abstract: A mass spectrometer system and a method of operating a mass spectrometer having an elongated rod set, the rod set having an entrance end, an exit end, a plurality of rods and a longitudinal axis, involving (a) admitting ions into the entrance end of the rod set; (b) producing an RF field between the plurality of rods to radially confine the ions in the rod set; (c) providing a static axial electric field within the rod set; and (d) separating the ions into a first group of ions and a second group of ions by providing an oscillating axial electric field within the rod set to counteract the static axial electric field, wherein the oscillating axial electric field varies along the longitudinal axis of the rod se.

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: In various embodiments, provided are ion optics systems comprising two or more pairs of ion condensers arranged 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 and wherein the deflection angle of each of the ion condensers is less than or equal to about ? radians.

Abstract: In a mass spectrometer, ions from an ion source pass through an inlet aperture into a vacuum chamber for transmitting prior to mass analysis by the mass analyzer. The configuration of the inlet aperture forms a sonic orifice or sonic nozzle and with a predetermined vacuum chamber pressure, a supersonic free jet expansion is created in the vacuum chamber that entrains the ions within the barrel shock and Mach disc. Once formed, an ion guide with a predetermined cross-section to essentially radially confine the supersonic free jet expansion can focus the ions for transmission through the vacuum chamber. This effectively improves the ion transmission between the ion source and the mass analyzer.

Abstract: A method of analyzing a substance comprises ionizing the substance to form a string of ions. The ions are then subject to a first mass analysis step. In one embodiment, the ions are accelerated into a collision cell in known manner to form primary fragment ions. These primary fragment ions are then accelerated into a downstream mass analyzer, to promote secondary fragmentation. In another embodiment of the invention, ions are passed through the collision cell, without fragmentation, and then accelerated from the collision cell into a low pressure section, which may be a mass analyzer or a rod set for collecting and collimating ions. This is done under conditions that promote fragmentation. The operating conditions of the low pressure section can be such as to promote collection or retention of ions depending upon their mass, and more specifically to reject low mass ions.

Abstract: In the field of mass spectrometry, a method and apparatus for fragmenting ions with a relatively high degree of resolution and efficiency. The technique includes trapping the ions in a linear ion trap, in which the background or neutral gas pressure is preferably on the order of 10?5 Torr. The trapped ions are resonantly excited for a relatively extended period of time, e.g., exceeding 50 ms, at relatively low excitation levels, e.g., less than 1 Volt(0-pk). The technique allows selective dissociation of ions with a high discrimination. High fragmentation efficiency may be achieved by superimposing a higher order multipole field onto the quadrupolar RF field used to trap the ions. The multipole field, preferably an octopole field, dampens the radial oscillatory motion of resonantly excited ions at the periphery of the trap. This reduces the probability that ions will eject radially from the trap thus increasing the probability of collision induced dissociation.

Abstract: The system for analyzing multiple samples includes a plurality of portable of sample supports each for accommodating a plurality of samples thereon, and an identification mechanism for identifying each sample location on each of the plurality of sample supports. The mass spectrometer is provided for analyzing each of the plurality of samples when positioned within a sample receiving chamber, and a laser source strikes each sample with a laser pulse to desorb and ionize sample molecules. The support transport mechanism provided provides for automatically inputting and outputting each of the sample supports from the sample receiving chamber of the mass spectrometer. A vacuum lock chamber receives the sample supports and maintains at least one of the sample supports within a controlled environment while samples on another of the plurality of sample supports are being struck with laser pulses.