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: 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 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 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 plate structure is provided including a retainer plate having a central opening, a sample insert plate which fits into the opening, an optional pressure plate and a handle. The handle applies pressure to the sample insert plate to retain it within the retainer plate. The sample insert plate is provided with a peripheral configuration, which assures that the sample insert plate is properly oriented within the sample plate support structure and is held flat. While the sample insert plate can be a consumable, the remaining portion of the apparatus can be reused.

Abstract: A sample plate structure is provided including a retainer plate having a central recess with a trough along its periphery, a sample insert plate which fits into and rests on contact surface of the recess, and a magnet that is held below the contact surface. A portion of the bottom surface of the insert is formed of a magnetic material. The magnet provides sufficient force to retain the insert plate in the retainer plate during MALDI MS analysis. The sample insert plate is provided with a peripheral configuration, which assures that the sample insert plate is properly oriented within the sample plate support structure and is held flat. A hole for a protrusion allows easy insert installation and alignment against the orientation feature in the recess as well as easy removal of the insert simply by pushing up from underneath the retainer plate. While the insert sample plate can be a consumable, the remaining portion of the apparatus can be reused.

Abstract: A chemical analysis method for determining chemically related differences between subject biological material such as genetically modified plant material and control biological material such as genetically unmodified plant material, which method includes at least the following six steps. The first step is to contact the subject biological material with a fluid extractant, such as a mixture of water, isopropanol and potassium hydroxide, to produce a fluid extract of the subject biological material. The second step is to contact the control biological material with the fluid extractant to produce a fluid extract of the control biological material. The third step is to chromatograph the fluid extract of the subject biological material, for example, gas or fluid chromatography, to produce a chromatogram of the fluid extract of the subject biological material.