Abstract: Systems and methods for analyzing compounds in a sample. In one embodiment, the present technology is directed towards a method of analyzing a sample, comprising: emitting ions from the sample; selectively filtering the emitted ions for at least one designated trigger ion; fragmenting the designated trigger ions; scanning for a designated trigger ion fragment; and upon detecting the designated trigger ion fragment, scanning for at least one confirmatory ion fragment.

Abstract: Methods for fragmenting ions retained in an ion trap are described. In various embodiments, a non-steady-state pressure of a neutral collision gas of less than about 5×10?4 Torr and an excitation amplitude of less than about 500 mV (peak to ground) is used to fragment ions with greater than about 80% fragmentation efficiency. In various embodiments, duration of ion excitation is greater than about 25 ms.

Abstract: Methods and kits for high throughput screening and analysis of metabolic disorders using a laser desorption ion source coupled to a mass analyzer (for example, MALDI) are provided. The metabolic disorders can be amino acid, organic acid or fatty acid oxidation disorders. A panel of disorders can be analyzed at high speeds. The methods and kits are particularly useful for newborn screening (NBS) of metabolic disorders.

Abstract: Methods for fragmenting ions in an ion trap are described.

Abstract: A method of operating an ion trap spectrometer system having an ion trap is provided.

Abstract: In a tandem mass spectrometer using a collision cell for ion fragmentation, the upper limit of the collision energy required for collision induced dissociation (CID) can be extended without reaching or going beyond the upper electrical discharge limit of the system components. The present teachings describe a method of lifting the potential energy of ions to a predetermined level sufficient for CID fragmentation while satisfying a discharge free condition. The present teaching also describes a method of lifting the potential energy of the fragment ions after CID fragmentation so that the product ions have sufficient energy for mass analysis.

Abstract: This relates to filter columns for isolating nucleic acids, particularly at small elution volumes. The filter column is adapted for stable placement within the upper portion of standard plastic collection tubes of various sizes. The body of the filter column has a number of surfaces to accommodate placement within variously sized collection tubes. The filter column contains nucleic acid-specific filter which can be located at alternate regions within the filter column, providing different filter surface areas and loading volume capacities using the same column body. The filter column has an opening on an upper end adapted to be sealed by a cap. A method for recovering nucleic acids using such filter column is also provided.

Abstract: The applicants' teachings provide methods, systems, and apparatus useful in operating mass spectrometers and other devices incorporating multipole rod sets or other multi-electrode devices to simultaneously contain ions of both positive and negative charges through the simultaneous application to the rods or other electrodes of both radio-frequency (RF) and alternating (AC) currents.

Abstract: Ion trap apparatus and methods for efficiently addressing the effects of charge space caused by ion trap overfilling, useful in linear ion traps of mass spectrometers.

Abstract: Improved systems, apparatus, methods, and programming useful for the automated analysis of complex compounds using mass spectrometers. Systems, apparatus, methods, and programming according to the invention provide for the automatic determination by a controller 54 of a mass spectrometer 14, 214 of an analysis operation to be implemented using the mass spectrometer, the analysis operation adapted specifically for analysis of one or more substances based contained within a compound based on identification of the compound and/or substances provided by a user of the spectrometer, and a database 66 or other library of information concerning suitable processes or process steps for analyzing substances.

Abstract: A mass spectrometer and a method of operating and building same is provided in which a hexapole component is deliberately added to a substantially quadrupole field. This can result in unwanted octopole and dipole fields also being added to the substantially quadrupole field. Modifications to the mass spectrometer as well as ways of operating the mass spectrometer are provided for dealing with the unwanted octopole and dipole fields.

Abstract: Methods for improved separation of ions from an ion trap employing a combination of low pressure and low amplitude ion excitation, including methods for removing, from an ion trap ion population, ions having a m/z value neighboring that of an ion of interest, mass spectrometry methods providing improved resolution of ion detection, and programmable apparatus programmed with instructions therefor.

Abstract: Systems, including compositions, kits, and methods, particularly for photoluminescence applications. The systems may include, among others, (1) organic chelators, (2) complexes between the chelators and lanthanide ions, and (3) precursors, derivatives, and uses thereof. The chelators may include a 1,4,7,10-tetraazacyclododecane ring system, for example, having the formula: Here, R1, R2, and R3 are substituents of the tetraazacyclododecane ring system, that is further substituted at the 10-position by a sensitizer Z that is typically a polyheterocyclic ring system. The organic chelator may be capable of forming a luminescent complex with a lanthanide ion, and is optionally further substituted by a reactive functional group or a conjugated substance. The resulting lanthanide complex may be useful in luminescence-based assays, such as energy transfer assays, among others.

Abstract: A method, system, kit and uses for quantifying and normalizing at least one product of ethanol metabolism are provided. A method is provided for quantifying and normalizing at least one product of ethanol metabolism in a sample comprising creatinine. The method comprises adding a predetermined amount of at least one internal standard to the sample; adding deuterated creatinine to the sample; detecting and measuring at least one product of ethanol metabolism, the predetermined amount of at least one internal standard in the sample, the deuterated creatinine, and the creatinine. The method also comprises quantifying the amount of at least one product of ethanol metabolism in the sample using the measurement of the at least one internal standard; quantifying the amount of creatinine in the sample using the measurement of the deuterated creatinine; and normalizing the quantity of the at least one product of metabolism using the measurement of the creatinine.

Abstract: Systems, including compositions and methods, for measuring pH, particularly in cells, organelles, and other samples. The compositions include pH-sensitive fluorescent and fluorogenic 2?,7?-dialkylfluorescein derivatives and associated nonfluorescent precursor compounds. The compositions may permit ratiometric measurement in the excitation spectrum and the emission spectrum. The methods include adding a precursor compound to a sample cell, incubating the sample cell to release the free indicator, illuminating the sample cell, and detecting the fluorescence response of the free indicator.

Abstract: A method of operating an ion trap spectrometer system having an ion trap is provided.

Abstract: There is provided a linear ion trap having an ion guide and a method of operating same. The ion guide has a first end and a second end. The method involves a) providing a first group of ions within the ion guide; b) providing a second group of ions within the ion guide, the second group of ions being opposite in polarity to the first group of ions; c) providing an RF drive voltage to the ion guide to radially confine the first group of ions and the second group of ions in the ion guide; d) providing a gas flow of an inert gas in a first axial direction away from the first end of the ion guide and toward a middle of the ion guide to repel both the first group of ions and the second group of ions from the first end of the ion guide; and, e) providing a trapping region barrier for repelling both the first group of ions and the second group of ions away from the second end of the ion guide.

Abstract: Systems and methods are described for processing of laser capture microdissection (LCM) samples. A biological sample processing system includes a laminated film sample processing device including a reaction chamber mated with a biological sample carrier to form a fluidic circuit. A multiple step fluidic device includes an LCM transfer film and a surface that is spaced apart from the transfer film so as to define a fluid volume. The reaction buffer can be removed through an exit port, or stop junction, in the surface. Advantages of the systems and methods include facilitating subsequent processing reducing the volume of reagents and enhancing economy. For instance, the reaction buffer can be conveniently removed away from the LCM transfer film.

Abstract: Systems and methods for automated laser microdissection are disclosed. A sample of biological material is located between a polymer membrane and a substrate. Targeted biological material is manually or automatically selected and a transfer film is placed in juxtaposition with the targeted biological material on the side of the polymer membrane. An infrared laser activates at least a portion of the transfer film such that the transfer film in the vicinity of targeted portion of biological material adheres onto the polymer membrane. The infrared laser is directed in a closed or substantially closed curve around the targeted portions or directly at the targeted portions. The transfer film is then separated removing the targeted portions of biological material which are adhered along with the membrane from the remaining portion of the tissue sample.

Abstract: A method of operating a mass spectrometer system having an ion trap is provided. The method comprises encoding a selected characteristic in at least one of the first group of precursor ions and the first plurality of fragments, wherein the encoding operation is applied to at least one of the first group of precursor ions and the first plurality of fragments without being applied to other ions such that the first plurality of fragment ions has the first selected characteristic and the other ions lack the first selected characteristic.