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: A time-of-flight mass spectrometer includes a pulsed ion source that generates a pulse of ions from a sample to be analyzed. An ion lens focuses the pulse of ions into an ion beam. An ion deflector deflects the ion beam into a deflected ion beam path. An ion mirror is positioned in the deflected ion beam path so that a plane of constant ion flight time is parallel to an input surface of the ion mirror. The ion mirror decelerates and then accelerates ions so that ions of like mass and like charge exit the ion mirror in a reflected ion beam and reach an ion detector at substantially the same time. An ion detector is positioned in the path of the reflected ion beam so that a plane of constant ion flight time is substantially parallel to an input surface of the ion detector. The ion detector detects a time-of-flight of ions from the pulsed ion source to the ion detector that is substantially independent of a path traveled.

Abstract: Many applications in the study of metabolics and proteomics require measurements on peptides and small molecules with high resolving power and mass accuracy. These are often present in complex mixtures and sensitivity over a relatively broad mass range, speed of analysis, reliability, and ease of use are very important. The present invention is a time-of-flight mass spectrometer providing optimum performance for these and similar applications.

Abstract: The present invention provides a time-of-flight (TOF) mass analyzer. The system includes an analyzer vacuum housing isolated from the evacuated ion source vacuum housing by a gate valve maintained at ground potential. A pulsed ion source is located within the ion source housing, and the gate valve is located in a first field-free region at ground potential. A second field-free drift space within the analyzer housing is biased at high voltage with opposite polarity to the voltage applied to the pulsed ion source. Novel ion detectors are provided with input surfaces in electrical contact with the second field-free drift space with output connected to an external digitizer at ground potential.

Abstract: The present invention is directed to ion source and vacuum housings for use in MALDI-TOF mass spectrometry which operates with any type of mass analyzer including linear, reflector, or tandem TOF-TOF instruments. By removing the requirement for the vacuum lock, the present invention allows operation of the ion source vacuum chamber at a pressure at least two orders of magnitude higher than conventional instruments. The present invention also requires only a single valve that isolates the ion source vacuum housing from the TOF analyzer vacuum housing. This is a significant improvement over vacuum locks in the art where the valve opening must be sufficiently large to allow the sample plate to pass through.

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: The invention comprises apparatus and methods for rapidly and accurately determining mass-to-charge ratios of molecular ions produced by a pulsed ionization source, and for fragmenting all of the molecular ions produced and rapidly and accurately determining the intensities and mass-to-charge ratios of the fragments produced from each molecular ion.

Abstract: The present invention provides a time-of-flight (TOF) mass analyzer. The system includes an analyzer vacuum housing isolated from the evacuated ion source vacuum housing by a gate valve maintained at ground potential. A pulsed ion source is located within the ion source housing, and the gate valve is located in a first field-free region at ground potential. A second field-free drift space within the analyzer housing is biased at high voltage with opposite polarity to the voltage applied to the pulsed ion source. Novel ion detectors are provided with input surfaces in electrical contact with the second field-free drift space with output connected to an external digitizer at ground potential.

Abstract: The present invention is directed to ion source and vacuum housings for use in MALDI-TOF mass spectrometry which operates with any type of mass analyzer including linear, reflector, or tandem TOF-TOF instruments. By removing the requirement for the vacuum lock, the present invention allows operation of the ion source vacuum chamber at a pressure at least two orders of magnitude higher than conventional instruments. The present invention also requires only a single valve that isolates the ion source vacuum housing from the TOF analyzer vacuum housing. This is a significant improvement over vacuum locks in the art where the valve opening must be sufficiently large to allow the sample plate to pass through.

Abstract: The TOF mass spectrometer disclosed places an even number of ion mirrors in close proximity to a MALDI ion source and a field-free drift space between the exit from the mirrors and an ion detector. This “reversed geometry” configuration may be distinguished from a conventional reflecting TOF analyzer employing a single ion mirror where a large fraction of the total drift space is located between the ion source and the mirror.

Abstract: The present invention comprises apparatus and methods for rapidly and accurately determining mass-to-charge ratios of molecular ions produced by a pulsed ionization source, and for fragmenting substantially all of the molecular ions produced while rapidly and accurately determining the intensities and mass-to-charge ratios of the fragments produced from each molecular ion.

Abstract: Many applications in the study of metabolics and proteomics require measurements on peptides and small molecules with high resolving power and mass accuracy. These are often present in complex mixtures and sensitivity over a relatively broad mass range, speed of analysis, reliability, and ease of use are very important. The present invention is a time-of-flight mass spectrometer providing optimum performance for these and similar applications.

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 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: The present invention is directed to improved systems and components for coupling separations technology with MALDI-TOF mass spectroscopy. Specifically, this invention provides new apparatus configurations and methods for interfacing liquid-phase separations with MALDI mass spectrometry. The present invention exploits and expands the use of the collimated hole structure (CHS) sample plate as an integral component of the interface.

Abstract: The present teachings relate to MALDI-TOF instruments, instrument components, and methods of operation thereof. In various aspects, the MALDI-TOF instrument can serve and be operated as a MS/MS instrument. In various embodiments, provided are MALDI-TOF instruments, and methods of operating one or more components of a MALDI-TOF instrument, that facilitate one or more of increasing sensitivity, increasing resolution, increasing dynamic mass range, increasing sample support throughput, and decreasing operational downtime.

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: 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: A mass spectrometer according to the present invention has an ionization source for generating ions; an ion trap for accumulating the ions; a time-of-flight mass spectrometer for performing mass spectrometry analysis on the ions by use of a flight time; a collision damping chamber disposed between the ion trap and the time-of-flight mass spectrometer and having a plurality of electrodes therein, which produce a multi-pole electric field, wherein a gas is introduced into the collision damping chamber to reduce kinetic energy of the ions ejected from the ion trap; and an ion transmission adjusting mechanism disposed between the ion trap and the collision damping chamber to allow or prevent injection of the ions from the ion trap to the collision damping chamber. The mass spectrometer provides greatly enhanced qualitative and quantitative analysis capabilities, as compared with conventional techniques.

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.