Abstract: A sample holder comprises a substrate microfabricated to define a multiplicity of microscopic islands defining sample support surfaces. At least one sump separates adjacent island surfaces and inhibits transport of samples between adjacent island surfaces.

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: 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 sample plate for MALDI-TOF mass spectrography is provided which consists of a collimated hole structure intimately connected to a frame. The frame and at least one surface of the collimated hole structure are electrically conductive. The collimated hole structure may be formed from any material including glass, plastic, and metal and at least one surface may be rendered conductive by application of a thin layer of an electrically conductive material such as a metal, metal oxide, carbon, or organic or inorganic conductor or semi-conductor. The conductive surface is maintained in good electrical conduct with the conductive frame.

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: 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: 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: 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: 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 MALDI plate construction is provided to support a sample in a manner to effect mass spectrometry of the sample. The plate construction comprises a sample receiving surface, a plate holder for retaining the sample receiving surface and an electrically conductive grid positioned adjacent to the sample receiving surface and in electrical contact with the plate holder.

Abstract: A tandem time-of-flight mass spectrometry including a pulsed ion generator, a timed ion selector in communication with the pulsed ion generator, an ion fragmentor in communication with the ion selector, and an analyzer in communication with the fragmentation chamber. The fragmentation chamber not only produces fragment ions, but also serves as a delayed extraction ion source for the analyzing of the fragment ions by time-of-flight mass spectrometry.

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 sample holder comprises a substrate microfabricated to define a multiplicity of microscopic islands defining sample support surfaces. At least one sump separates adjacent island surfaces and inhibits transport of samples between adjacent island surfaces.