Abstract: A tandem TOF mass spectrometer includes a first TOF mass analyzer that generates an ion beam comprising a plurality of ions and that selects a group of precursor ions from the plurality of ions. A pulsed ion accelerator accelerates and refocuses the selected group of precursor ions. An ion fragmentation chamber is positioned to receive the selected group of precursor ions that is refocused by the pulsed ion accelerator. At least some of the selected group of precursor ions is fragmented in the ion fragmentation chamber. A second TOF mass analyzer receives the selected group of precursor ions and ion fragments thereof from the ion fragmentation chamber and separates the ion fragments and then detects a fragment ion mass spectrum.

Abstract: A time-of-flight mass spectrometer includes a sample plate that supports a sample for analysis. A pulsed ion source generates a pulse of ions from the sample positioned on the sample plate. An ion accelerator receives the pulse of ions generated by the pulsed ion source and accelerates the ions. An ion detector includes an input in a flight path of the accelerated ions emerging from the field-free drift space and an output that is electrically connected to the sample plate. The ion detector converts the detected ions into a pulse of electrons.

Abstract: A time-of-flight mass spectrometer includes an ion source that generates ions. A two-field ion accelerator accelerates the ions through an ion flight path. A pulsed ion accelerator focuses the ions to a first focal plane where the ion flight time is substantially independent to first order of an initial velocity of the ions prior to acceleration. An ion reflector focuses ions to a second focal plane where the ion flight time is substantially independent to first order of an initial velocity of the ions prior to acceleration. An ion detector positioned at the second focal plane detects the ions. The two-field ion accelerator and the ion reflector cause the ion flight time to the ion detector for the ion of predetermined mass-to-charge ratio to be substantially independent to first order of both the initial position and the initial velocity of the ions prior to acceleration.

Abstract: A time-of-flight mass spectrometer includes an ion source that generates ions. A two-field ion accelerator receives the ions generated by the ion source and generates an electric field that accelerates the ions through an ion flight path. A pulsed ion accelerator generates an accelerating electric field that focuses the ions to a focal plane where the ion flight time to the focal plane for an ion of predetermined mass-to-charge ratio is substantially independent to first order of an initial velocity of the ions prior to acceleration. An ion detector is positioned at the focal plane to detect ions. The two-field ion accelerator generates electric fields that cause the ion flight time to the ion detector for an ion of predetermined mass-to-charge ratio to be substantially independent to first order of both the initial position and the initial velocity of the ions prior to acceleration.

Abstract: A tandem time-of-flight mass spectrometer includes a first pulsed ion source that produces ions with a first mass and charge that directs the ions into a first stage of a tandem TOF mass spectrometer. In addition, a second pulsed ion source produces ions with a second mass and an opposite charge directs the ions into the first stage of the tandem TOF mass spectrometer. A field-free reaction region is positioned in the ion flight path so that ions from first and second pulsed ion source arrive at the entrance of the field-free reaction region substantially simultaneously in at least one of time and space. At least some of the ions from the first and second pulsed ion source are fragmented by ion-ion collision between positive and negative ions. A second stage of the tandem mass spectrometer separates fragment ions produced in the reaction region according to their mass-to-charge ratio.

Abstract: A tandem TOF mass spectrometer includes a first TOF mass analyzer that generates an ion beam comprising a plurality of ions and that selects a group of precursor ions from the plurality of ions. A pulsed ion accelerator accelerates and refocuses the selected group of precursor ions. An ion fragmentation chamber is positioned to receive the selected group of precursor ions that is refocused by the pulsed ion accelerator. At least some of the selected group of precursor ions is fragmented in the ion fragmentation chamber. A second TOF mass analyzer receives the selected group of precursor ions and ion fragments thereof from the ion fragmentation chamber and separates the ion fragments and then detects a fragment ion mass spectrum.

Abstract: A time-of-flight mass spectrometer includes an ion source that generates ions. A two-field ion accelerator receives the ions generated by the ion source and generates an electric field that accelerates the ions through an ion flight path. A pulsed ion accelerator generates an accelerating electric field that focuses the ions to a focal plane where the ion flight time to the focal plane for an ion of predetermined mass-to-charge ratio is substantially independent to first order of an initial velocity of the ions prior to acceleration. An ion detector is positioned at the focal plane to detect ions. The two-field ion accelerator generates electric fields that cause the ion flight time to the ion detector for an ion of predetermined mass-to-charge ratio to be substantially independent to first order of both the initial position and the initial velocity of the ions prior to acceleration.

Abstract: A time-of-flight mass spectrometer includes an ion source that generates ions. A two-field ion accelerator accelerates the ions through an ion flight path. A pulsed ion accelerator focuses the ions to a first focal plane where the ion flight time is substantially independent to first order of an initial velocity of the ions prior to acceleration. An ion reflector focuses ions to a second focal plane where the ion flight time is substantially independent to first order of an initial velocity of the ions prior to acceleration. An ion detector positioned at the second focal plane detects the ions. The two-field ion accelerator and the ion reflector cause the ion flight time to the ion detector for the ion of predetermined mass-to-charge ratio to be substantially independent to first order of both the initial position and the initial velocity of the ions prior to acceleration.

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: A tandem time-of-flight mass spectrometer includes a first TOF mass analyzer that generates an ion beam comprising a plurality of precursor ions and that selects a group of precursor ions from the plurality of precursor ions. A first pulsed ion accelerator accelerates the selected group of precursor ions. A first ion fragmentation chamber fragments at least some of the selected group of precursor ions. A second pulsed ion accelerator accelerates the selected group of precursor ions and fragments thereof. A second ion fragmentation chamber further fragments at least some of the selected group of precursor ion fragments. A second TOF mass analyzer separates the fragments and detects a fragment ion mass spectrum.

Abstract: A tandem time-of-flight mass spectrometer includes a first pulsed ion source that produces ions with a first mass and charge that directs the ions into a first stage of a tandem TOF mass spectrometer. In addition, a second pulsed ion source produces ions with a second mass and an opposite charge directs the ions into the first stage of the tandem TOF mass spectrometer. A field-free reaction region is positioned in the ion flight path so that ions from first and second pulsed ion source arrive at the entrance of the field-free reaction region substantially simultaneously in at least one of time and space. At least some of the ions from the first and second pulsed ion source are fragmented by ion-ion collision between positive and negative ions. A second stage of the tandem mass spectrometer separates fragment ions produced in the reaction region according to their mass-to-charge ratio.

Abstract: A mass spectrometer includes a pulsed ion source that generates an ion beam comprising a plurality of ions. A first timed ion selector passes a first group of ions. A first ion mirror generates a reflected ion beam comprising the first group of ions that at least partially compensates for an initial kinetic energy distribution of the first group of ions. A second timed ion selector passes a second group of ions. A second ion mirror generates a reflected ion beam comprising the second group of ions that at least partially compensates for an initial kinetic energy distribution of the second group of ions. A timed ion deflector deflects the second group of ions to a detector assembly comprising at least two ion detectors which detects the deflected ion beam.

Abstract: A tandem TOF mass spectrometer includes a pulsed ion source that generates a pulse of precursor ions from a sample to be analyzed. A first pulsed ion accelerator accelerates and refocuses a predetermined group of precursor ions. A first timed ion passes the predetermined group of precursor ions and rejects substantially all other ions. An ion fragmentation chamber fragments at least some of the precursor ions in the predetermined group. A second timed ion selector selects a predetermined range of masses centered on each precursor in the predetermined group and rejects substantially all other ions. A second pulsed ion accelerator accelerates and refocuses the selected precursor ions and fragments thereof. An ion mirror generates a reflected ion beam.

Abstract: A tandem TOF mass spectrometer includes a first TOF mass analyzer that generates an ion beam comprising a plurality of ions and that selects a group of precursor ions from the plurality of ions. A pulsed ion accelerator accelerates and refocuses the selected group of precursor ions. An ion fragmentation chamber is positioned to receive the selected group of precursor ions that is refocused by the pulsed ion accelerator. At least some of the selected group of precursor ions is fragmented in the ion fragmentation chamber. A second TOF mass analyzer receives the selected group of precursor ions and ion fragments thereof from the ion fragmentation chamber and separates the ion fragments and then detects a fragment ion mass spectrum.

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: Accordingly, systems and methods for protein identification are provided. The present teaching provide for a system with one protein identification methodology based on one method and a second protein identification methodology based on a second protein identification methodology to interact and increase confidence in protein identification. Various embodiments employ protein identification methodologies that identify portions of a peptide. Various embodiments provide for a hypothesis generation module that can suggest modifications for the peptide based on differences between experimental and theoretical values. Various embodiments provide for an identifier module that can select one or more hypotheses from the hypothesis module as most probable. In this way, the present teachings can provide for systems and methods to combine protein identification results from multiple protein identification methodologies with the possibility of identifying modifications.

Abstract: A mass spectrometer includes a pulsed ion source that generates an ion beam comprising a plurality of ions. A first timed ion selector passes a first group of ions. A first ion mirror generates a reflected ion beam comprising the first group of ions that at least partially compensates for an initial kinetic energy distribution of the first group of ions. A second timed ion selector passes a second group of ions. A second ion mirror generates a reflected ion beam comprising the second group of ions that at least partially compensates for an initial kinetic energy distribution of the second group of ions. A timed ion deflector deflects the second group of ions to a detector assembly comprising at least two ion detectors which detects the deflected ion beam.

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: 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 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.