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Recent Patents of Interest in Proteomics: Sep 4, 2008

US Patent 7,418,352. Method of using data binning in the analysis of chromatography/spectrometry data. Inventors: Robert Plumb; Chris Stumpf; Marc Gorenstein. Assignee: Waters Investments
Invention pertains to a method of analyzing 3D data from a chromatography/spectrometry process, in particular an LC/MS process using a 2D multi-variant statistical analysis. LC/MS provides at least three pieces of information, but principal component analysis is typically performed using only 2D data and at least one parameter of data from LC/MS operation is lost. According to the authors, the method they developed preserves all three mathematical dimensions. 

US Patent 7,413,862. FRET probes and methods for detecting interacting molecules. Inventors: Jacobus Johannes Maria van Dongenò Frank Jakob Theodor Staal. Assignee: Erasmus Universteit Rotterdam
Invention pertains to the detection of interacting molecules. Provided is a set of a first and second probe, each having a dye allowing energy transfer. At least one probe has a reactive group allowing juxtapositioning of the first and second probe. A method is also provided for detecting at least two interacting molecules at the single-cell level.

US Patent 7,412,334. Mass spectrometer and method for enhancing resolution of mass spectra. Inventors: John Christian Fjeldsted; August Jon Hidalgo; William Daniel Frazer. Assignee: Agilent Technologies
Described is a mass spectrometer comprising an ion detector, an analog-to-digital converter, a sample adjuster, and an adder. The A/D converter is configured to receive and sample an analog sample from the ion detector, providing a plurality of samples. “The sample adjuster is configured to identify a peak defined by the samples and to suppress at least one of the samples of the peak such that a resolution of a peak within the mass spectrum is enhanced,” according to the abstract.

US Patent 7,411,183. User customizable plate handling for MALDI mass spectrometry. Inventors: Gregor Overney; Bryan Miller. Assignee: Agilent Technologies
Provided are methods for specifying the layout of a MALDI plate. It involves creating a file containing sample plate layout parameters that describe the layout of a MALDI sample plate and storing the file on a computer-readable medium before placing the MALDI sample plate into a MALDI ion source. 

US Patent 7,410,559. Electrophoresis methods. Inventors: Mari Tabuchi; Yoshinobu Baba. Assignee: Japan Science and Technology Agency
Provided are “a separation carrier comprising beta-1,3-glucan and/or methyl cellulose; a running buffer comprising the separation carrier; a method of capillary electrophoresis or microchip electrophoresis, wherein a sample comprising macromolecular compounds is run in the presence of the running buffer; a method of capillary electrophoresis or microchip electrophoresis, comprising the step of injecting the sample by an electrical injection or application of pressure; and a method for analyzing macromolecular compounds by the method of capillary electrophoresis or microchip electrophoresis,” according to the abstract. High resolution is able to be achieved quickly, according to the inventors, so the methods described are useful for proteomic analysis, high-throughput screening of proteins or sugar chains in gene analysis, and other applications.

US Patent 7,409,880. System useful for holding a sample and in subjecting the sample to chromatographic analysis. Inventors: John Hale; Michael Kneirman; Kirk Boraas. Assignee: Indiana Proteomics Consortium
A robotic system for handling components during chromatographic analysis of a sample is described. It includes a holder for positioning the sample within a separation pathway.

US Patent 7,409,298. Matched filtration with experimental noise determination for denoising, peak picking and quantitation in LC-MS. Inventors: Victor Andreev; Tomas Rejtar; Barry Karger. Assignee: Northeastern University
Described is “an improved system and method of analyzing sample data that increases the reliability of peak (compound) detection and identification in the presence of chemical and/or random noise,” according to the abstract. The system includes a compound-separating unit for separating constituent compounds in a sample mixture, a compound-analyzing unit for identifying and quantitating at least one of the separated compounds, and a computer for gathering data from the compound-separating and -analyzing units, and for generating a multi-dimensional data set incorporating the acquired data.

US Patent 7,409,296. System and method for scoring peptide matches. Inventors: Jacques Colinge; Alexandre Masselot. Assignee: Geneva Bioinformatics
Described is a system and method for scoring peptide matches. The invention improves identification of peptides and proteins by introducing an appropriate signal detection-based scoring system “and what is believed to be the new concept of an extended match,” according to the abstract.

US Patent 7,408,152. Ion source using matrix-assisted laser desorption/ionization. Inventors: Armin Holle; Jens Hohndorf; Andreas Haase; Markus Kayser. Assignee: Bruker Daltonics
The ion source comprises a MALDI sample support and a solid-state laser system “generating a pulsed laser beam, which has a wavelength in the range between 332 and 342 nanometers and is spatially shaped in the solid-state laser system such that the spatial intensity distribution of the laser beam on the MALDI sample support exhibits more than one intensity peak,” according to the abstract.

The Scan

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Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.