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: A mass spectrometer system including a differential mobility spectrometer and a mass spectrometer at least partially sealed to, and in fluid communication, with, the differential mobility spectrometer, together with a related method, are provided. The mass spectrometer system can be operable to, and method can comprise, a) maintaining the differential mobility spectrometer at an internal operating pressure; b) providing ions to the differential mobility spectrometer; c) maintaining the mass spectrometer at a vacuum pressure lower than the internal operating pressure to draw a gas flow including the ions through the differential mobility spectrometer and into the vacuum chamber; and, d) modifying the gas flow between the differential mobility spectrometer and the mass spectrometer to change a gas flow rate through the differential mobility spectrometer.

Abstract: A mass analysis system including a low pressure dissociation region and a differential mobility spectrometer. The differential mobility spectrometer including at least one pair of filter electrodes defining an ion flow path where the filter electrodes generate an electric field for passing through a selected portion of the sample ions based on the mobility characteristics of the sample ions. The differential mobility spectrometer also includes a voltage source that provides DC and RF voltages to at least one of the filter electrodes to generate the electric field, an ion inlet that receives sample ions that have passed through the low pressure dissociation region, and an ion outlet that outputs the selected portion of the sample ions. A mass spectrometer receives some or all of the selected portion of the sample ions.

Abstract: Methods for cooling ions retained in an ion trap are described. In various embodiments, a cooling gas is delivered into a linear ion trap causing a non-steady state pressure elevation in at least a portion of the trap above about 8×10?5 Torr for a duration less than the ion-retention time. In various embodiments, the duration of pressure elevation can be based upon a period of time required for an ion to lose a desired amount of its kinetic energy.

Abstract: Methods and compositions relating to the generation and use of gene expression data from tissue samples that have been fixed and embedded are provided. The data can electronically stored and implemented as well as used to augment diagnosis and treatment of diseases.

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: A mass analyzer system includes an ion inlet that receives a flow of ions, a multi-mode ion controller that controls some or all of the ions, and a multi-mode mass analyzer, in communication with the ion controller, that performs at least one of analyzing and controlling some or all of the ions. The system also includes a detector, in communication with the multi-mode mass analyzer, that detects some or all of the ions and a processor that controls the operation of at least one of the multi-mode ion controller and the multimode mass analyzer.

Abstract: Methods and systems for counting nuclei for cells in a cell-containing sample are disclosed, such as carried out on a computer. The methods comprise: receiving a raw image of the cell-containing sample; transforming the raw image into a segmented image comprising one or more nuclei clusters. The methods further comprise: for each of the one or more nuclei clusters, obtaining a convex hull of the nuclei cluster; locating any indentations on the nuclei cluster by comparing the nuclei cluster to the convex hull of the nuclei cluster; calculating a first nuclei count based on a tally of the indentations; and assigning the nuclei cluster to a cell among the plurality of cells. The methods further comprise: calculating a second nuclei count for each cell by totaling the first nuclei counts of its constituent nuclei clusters; and presenting a result based on the second nuclei count for at least one of the plurality of cells.

Abstract: Methods and compositions relating to the generation and use of gene expression data from tissue samples that have been fixed and embedded are provided. The data can electronically stored and implemented as well as used to augment diagnosis and treatment of diseases.

Abstract: A method of operating a mass spectrometer having an elongated rod set and a set of auxiliary electrodes is provided, the rod set having an entrance end and an exit end and a longitudinal axis. The method comprises a) admitting ions into the entrance end of the rod set; b) trapping at least some of the ions in the rod set by producing a barrier field at an exit member adjacent to the exit end of the rod set and by producing an RF field between the rods of the rod set; and, c) providing an auxiliary AC excitement voltage to the set of auxiliary electrodes to energize a first group of ions of a selected mass to charge.

Abstract: A method and apparatus for multiplexing ions in an MSn mass spectrometer is provided. Ion are filtered to produce a group of ions of interest, the group of ions below a space charge limit of the MSn mass spectrometer. At least a portion of the group of ions are fragmented to form a fragmented group of ions. At least a portion of the fragmented group are stored such that a plurality of portions of the fragmented group can be sequentially selected for mass spectrometry analysis. Each of the plurality of portions of the fragmented group are sequentially selected and re-fragmented prior to mass spectrometry analysis. Each of the plurality of portions of the fragmented group are analyzed, via mass spectrometry, once each of the plurality of portions of the fragmented group has been fragmented.

Abstract: A method for introducing samples through a boundary member partially defining a chamber at an entrance point coaxial to a sampling inlet of a mass spectrometer is described. Field-free conditions can be established in at least one region of the chamber. The sample can be introduced adjacent to the sampling inlet, and introducing at least a second sample can be introduced through at least one other entrance point in the chamber not adjacent to the sampling inlet. An apparatus having a sampling inlet and a boundary member partially defining a chamber is also described. Field-free conditions can be established in at least one region of the chamber, and there can be a first aperture in the boundary member through which a source emits sample. Related devices, uses and mass spectrometers are also described.

Abstract: Photometric methods for determining optical pathlength of liquid samples containing analytes dissolved or suspended in a solvent are provided that rely on determining a relationship between the light absorption properties of the solvent and the optical pathlength of liquid samples containing the solvent. This relationship is used to establish the optical pathlength for samples containing an unknown concentration of analyte but having similar solvent composition. Methods are also provided for determining the concentration of analyte in such samples where both the optical pathlength and the concentration of analyte are unknown. The methods may rely on separately determining, at different wavelengths of light, light absorption by the solvent and light absorption by the analyte. Light absorption by the analyte, together with the optical pathlength so determined, is used to calculate the concentration of the analyte.

Abstract: Systems and methods for reducing background noise in a mass spectrum. The method includes the following steps of: (a) obtaining an original mass spectrum; (b) determining a noise mass spectrum corresponding to background noise in the original mass spectrum; and (c) determining a corrected mass spectrum by subtracting the noise mass spectrum from the original mass spectrum. Step (b) of the method may include the steps of: A) effecting a transformation of the original mass spectrum into the frequency domain to obtain an original frequency spectrum; B) identifying at least one dominant frequency in the original frequency spectrum; C) generating a noise frequency spectrum by selectively filtering for said dominant frequencies; and D) determining the noise mass spectrum by effecting a transformation of the noise frequency spectrum into the mass domain.

Abstract: Systems for detecting molecular modifications and the presence and/or activity of enzymes and/or other agents involved in facilitating or otherwise regulating such modifications.

Abstract: A mass spectrometer having an elongated rod set, the rod set having a first end, a second end, a plurality of rods and a central longitudinal axis is described as is a method operating same.

Abstract: A mass spectrometer system including a differential mobility spectrometer and a mass spectrometer at least partially sealed to, and in fluid communication, with, the differential mobility spectrometer, together with a related method, are provided. The mass spectrometer system can be operable to, and method can comprise, a) maintaining the differential mobility spectrometer at an internal operating pressure; b) providing ions to the differential mobility spectrometer; c) maintaining the mass spectrometer at a vacuum pressure lower than the internal operating pressure to draw a gas flow including the ions through the differential mobility spectrometer and into the vacuum chamber; and, d) modifying the gas flow between the differential mobility spectrometer and the mass spectrometer to change a gas flow rate through the differential mobility spectrometer.

Abstract: A system including a differential mobility spectrometer is described as is a method of operating the system including the differential mobility spectrometer.

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.

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.