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: An apparatus and method is disclosed for reducing contamination in a mass spectrometer instrument system. The system includes an ion source at a first pressure for generating ions by laser desorption/ionization and an inlet aperture to a vacuum chamber at a second, lower pressure than the first pressure of the ion source. A sample plate within the ion source supports a sample deposited thereon and a laser can be configured to generate laser pulses striking at least a portion of the sample at an angle of incidence from about 0 to about 80 degrees to the center line of a first ion optical axis of a mass analyzer, producing a plume. A combination of the angle of incidence of the laser pulses and the distance between the sample plate and the inlet region aperture can reduce neutral contaminants in the plume from being drawn into the inlet aperture.

Abstract: In various aspects, ion sources, mass spectrometer systems, and a power supply circuit coupled to a feedback circuit are provided. A power supply is provided that includes at least the power supply circuit and is operable to transfer charge to a load. The feedback circuit is responsive to a DC component of an output voltage supplied by the power supply in a first feedback loop and an AC component of the output voltage in a second feedback loop to produce a feedback signal representative of at least one of: a value of the output voltage before a charge transfer from a capacitor of the power supply to a load; the value of the output voltage during the charge transfer from the capacitor of the power supply to the load; or the value of the output voltage after the charge transfer from the capacitor of the power supply to the load.

Abstract: A method of operating a mass spectrometer having a rod set is provided. The rod set has a first end, a second end opposite to the first end, and a longitudinal axis extending between the first end and the second end.

Abstract: A method for dynamic pixel mass spectrometric imaging, or dynamic pixel imaging is disclosed. The method includes striking a sample to be scanned with a laser beam so that the laser beam releases analytes from the sample. The laser beam and the sample are then displaced relative to one another so that the laser beam substantially continuously traces a predefined path on the sample to release analytes from the sample along the predefined path. A mass analysis of the released analytes is performed.

Abstract: Computer-implementable methods consistent with the present teachings can be used in the design of selective- and multiple-reaction monitoring experiments for the identification of proteins and peptides of interest. By determining candidate parent-daughter ion transition pairs and scoring the pairs based on their ability to be detected experimental design time can be reduced and with a more focused list of transition pairs more experiments can be run successfully in a given period of time.

Abstract: A method of analyzing ions is provided having a first ion guide with first and second ends and introducing a first group of ions and a second group of ions of opposite polarity into the first ion guide, and applying an RF voltage potential to the first ion guide for confining the first and second groups of ions radially within the first ion guide. A first trapping barrier is provided to the first end of the first ion guide for trapping the first group of ions within the first ion guide and a second trapping barrier is provided to the second end of the first ion guide for trapping the second group of ions within the first ion guide and an axial field is provided for pushing the first group of ions toward the first trapping barrier and pushing the second group of ions toward the second trapping barrier.

Abstract: The invention provides a multipole ion trap. The trap has a longitudinal axis. An oscillating on-axis potential is set up along the longitudinal axis, providing a potential well in which ions are trapped. In some embodiments, rods forming the poles are symmetrically and equidistantly positioned about the longitudinal axis and RF signal with different magnitudes are applied to the poles. In other embodiments, the rods are not positioned symmetrically about the longitudinal axis and the RF signals applied to the poles may have the same or different magnitudes. Poles used in the invention may include two or more rods. An ion trap according to the invention may include more than two poles, and in some embodiments, a third or additional pole may be added to provide the oscillating on-axis potential. The ion trap may be used mass selectively scan ions, fragment ions and to trap and separate differently charged ions, among other uses.

Abstract: The present teachings provide methods for the development of a mass spectrometric based assay for a protein in a sample using parent-daughter ion transition monitoring (PDITM). In various aspects, the present teachings provide methods for developing a mass spectrometric based assay for a protein in a sample without the use of a standard for the protein. In various embodiments, the sample comprises proteolytic fragments of a protein which is present in low abundance in the physiological fluid from which it is derived.

Abstract: In various embodiments, provided are ion optical assemblies, and systems for mounting and aligning ion optic components. In various embodiments, the present teachings provide ion optical assemblies with features that facilitate the alignment of ion optical elements. In various embodiments, the alignment of the ion optical elements by compressing them with securing members, as described in the present teachings, can simplify the alignment and assembly of ion optical elements. In the present teachings, no torque pattern is required to compress and align the ion optical elements. In various embodiments, the present teachings provide systems for mounting and aligning ion optic components that facilitate their alignment.

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: 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 mass spectrometer and a method of operating same is provided. The mass spectrometer has an elongated rod set. The rod set has an entrance end and an exit end. An RF drive voltage is applied to the rod set to radially confine a first group of ions and a second group of ions of opposite polarity in the rod set. An entrance auxiliary RF voltage is applied to the entrance end and an exit auxiliary RF voltage to the exit end relative to the RF drive voltage, to trap both the first group of ions and the second group of ions in the rod set.

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: A mass spectrometer system having an ion trap and a downstream mass spectrometer is provided. A plurality of groups of ions are provided to the ion trap and a first mass-to-charge ratio is selected. The downstream mass spectrometer is configured to filter out one of (i) ions having a first unselected mass-to-charge ratio different from the first mass-to-charge ratio, and (ii) mass signals for ions having the first unselected mass-to-charge ratio different from the first mass-to-charge ratio.

Abstract: An apparatus and method for dispensing low volumes of an analyte solution. The apparatus comprises: (a) a receiver defining an ejection cavity and an outlet downstream of and in fluid communication with the ejection cavity; (b) first and second fluid conduits coupled to the receiver and defining respective first and second fluid flow paths in fluid communication with the ejection cavity; (c) an analyte generating apparatus operatively coupled to the first fluid conduit and operable to deliver analyte solution along the first fluid flow path to the ejection cavity; and (d) a dispensing mechanism operatively coupled to the second fluid conduit and operable to deliver a fluid buffer along the second fluid flow path into the ejection cavity to displace analyte solution present therein through the outlet. The method involves filling the ejection cavity with an analyte solution at a selected rate and injecting a fluid buffer into the injection cavity to displace the analyte solution through the outlet.

Abstract: In the field of mass spectrometry, a method of obtaining a mass spectrum enriched with fragment ions while retaining the precursor ion. The technique includes varying the collision energy experienced by the precursor ion such that a range of fragmentations occur. Related methods are also disclosed for obtaining MS, MS2, MS3 and MSn spectra which are enriched with fragment ions.

Abstract: A mass analyzer for use in a mass spectrometry system comprises an elongate rod set. The rod set has first and second ends and an inscribed circle within the rod set. The radius of the rod set varies from one end of the rod set to the other, so that ions of different mass to charge ratios will become unstable at different locations along the rod set. This characteristic can then be used to cause ejection of ions at different locations along the rod set, in a mass dependent manner. Detectors placed linearly along the rod set can then be used to detect ions and determine the mass of the ions from their ejection locations.

Abstract: A multi-device interface for use in mass spectrometry for interfacing one or more ion sources to one or more downstream devices. The multi-device interface comprises three or more multipole rod sets configured as either an input rod set or an output rod set depending on potentials applied to the multipole rod sets. The multipole rod sets configured as an input rod set are connectable to the one or more ion sources for receiving generated ions therefrom and sending the ions to at least one multipole rod set configured as an output multipole rod set. The output multipole rod sets are connectable to a downstream device for sending the generated ions thereto. At least two of the multipole rod sets are configured as input rod sets or at least two of the multipole rod sets are configured as output rod sets.

Abstract: A mass spectrometer has an ion source for producing sample ions. The ions pass through an ion interface, to a reaction/collision cell section. An ion-neutral decoupling device is provided between the ion interface and the reaction/collision cell section, to provide substantial separation between ions and neutral particles. The supersonic jet entering the spectrometer can have sufficient energy to cause the plasma gases, such as argon, to overcome the pressure differential between the reaction/collision cell and an upstream section of the spectrometer so as to penetrate into the reaction/collision cell; the decoupling device prevents this. The decoupling device can have offset apertures provided by plates or rods or other comparable arrangements, or can comprise a quadrupolar electrostatic deflector, an electrostatic sector deflector or a magnetic sector deflector.