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Recent Patents of Interest in Proteomics: Apr 16, 2009

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US Patent 7,519,514. Systems and methods for removing noise from spectral data. Inventor: Randy Keith Roushall. Assignee: Agilent Technologies

In the method described, a noise burst level is defined, and if a spectral point has an intensity point greater than the burst level, points neighboring the burst point are examined. "If a function of these neighboring points indicates that the burst point is a discrete event, then the abundance level of the burst point is altered," according to the abstract.


US Patent 7,518,108. Electrospray ionizationion source with tunable charge reduction. Inventors: Brian L Frey; Lloyd M Smith; Michael S Westphall. Assignee: Wisconsin Alumni Research Foundation

Methods, devices, and device components are provided for preparing ions from liquid samples containing species and methods and devices for analyzing chemical species in liquid samples. The invention also provides an ion source for generating analyte ions "having a selected charge-state distribution, such as a reduced charged state distribution, that may be effectively interfaced with a variety of charged particle analyzers, including virtually any type of mass spectrometer," according to the abstract.


US Patent 7,517,496. Latex-based adsorbent chip. Inventor: Christopher A Pohl. Assignee: Bio-Rad Laboratories

The chip described includes three components: a substrate, an intermediate layer of linker arms, and an adsorbent film that is attached to the linker arms. Also provided is a method for making the chips "in which the substrate-intermediate film cassette is formed and the absorbent film is subsequently immobilized thereon," according to the abstract. When the adsorbent film is from the same preparation across a particular batch of chips, the chips enable data acquisition that is "highly reproducible from one chip to the next throughout the particular batch of chips," the inventors said in the abstract. The patent also provides methods for using the chips to perform assays.


US Patent 7,514,676. Method and apparatus for selective filtering of ions. Inventors: Jason S Page; Keqi Tang; Richard Smith. Assignee: Battelle Memorial Institute

Pertains to a low m/z filter that employs electrospray ionization to block ions associated with unwanted low m/z species from entering the mass spectrometer and "contributing their space charge to downstream ion-accumulation steps," according to the abstract. The filter provides a linear voltage adjustment of low-mass filtering from m/z values of about 50 to 500. Though filtering above 500 can be done, higher m/z species are attenuated.


US Patent 7,514,000. Implementation of microfluidic components, including molecular fractionation devices, in a microfluidic system. Inventors: John R Gilbert; Manish Deshpande; Jaishree Trikha. Assignee: Cytonome

Described is a system and method for integrating microfluidic components in a microfluidic system that enables the system to perform a selected function. A capping module includes a microfluidic element to perform a microfluidic function. The microfluidic element may comprise a matrix having affinity for selected molecules in a sample. "The matrix binds, reacts with, and/or retains the selected molecules without affecting other molecules in the sample," according to the abstract.


US Patent. 7,512,524. Preparing peptide spectra for identification. Inventors: Ilan Be'er; Eilon Barnea; Emanuel Gofman. Assignee: International Business Machines

A method is described that includes the construction of a symmetric distance matrix from a plurality of peptide spectra. A cluster of at least one of the spectra is represented in the row of the matrix and is represented in a column of the matrix. The method calls for finding the minimum of each of the clusters in the matrix, constructing a vector for the minima "where each element in the vector corresponds to one of the clusters," and finding the global minimum of the matrix as being the minimum of the vector, according to the abstract. Two of the clusters identified by the global minimum are merged and at least one peptide associated with the merged cluster is identified.

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US Patent 7,511,267. Data-dependent accurate mass neutral loss analysis. Inventors: Vladimir Zabrouskov. Assignee: Thermo Finnigan [now called Thermo Fisher Scientific]

A method is described in which candidate product ions are selected by identifying peaks in an MS/MS spectrum "acquired in a first-mass analyzer that exhibits a specified nominal neutral-loss value, which may be representative of the mass of a peptide modification," according to the abstract. High-mass accuracy MS and MS/MS spectra acquired at a second mass analyzer are processed to "determine if the mass difference between a candidate product ion and its corresponding precursor matches an accurate neutral-loss value," the authors said.


US Patent 7,511,155. Reagents and a method for saturation-labeling of proteins. Inventors: Karen Williams; Timothy Stone; Adrian Christopher Simmonds; Claire Alison Sweet; Susan Janet Fowler. Assignee: GE Healthcare

Provided is a matched set of fluorescent dyes in which each dye can covalently attach to a protein and each dye has a molecular structure and charge that is matched with the other, such that "relative electrophoretic mobility of a protein labeled with one dye of the set is the same as the electrophoretic mobility of the protein labeled with a different dye of the set," according to the abstract. Also provided is a method for saturation labeling of a protein with a fluorescent dye "so as to label all available target amino acid, suitably cysteine, residues in the protein, thereby giving a single population of labeled protein molecules."


US Patent 7,510,842. Biomarker for ovarian and endometrial cancer: hepcidin. Inventors: Vladimir Podust; Zhen Zhang; Eric T Fung; Robert Bast; Daniel W Chan; Jin Song. Assignees: Vermillion; Johns Hopkins University; Board of Regents, the University of Texas System

Pertains to protein biomarkers and biomarker combinations useful in the identification of ovarian and endometrial cancers. The patent claims that hepcidin has been found to be a biomarker for both ovarian and endometrial cancers and that a panel of biomarkers including hepcidin, transthyretin, and optionally other markers, "are useful to classify a subject sample as ovarian cancer or non-ovarian cancer," according to the abstract.


US Patent 7,507,955. Mass spectrometer multipole device. Inventors: Robert K Crawford; James Bertsch. Assignee: Agilent Technologies

The invention provides a multipole device for a mass spectrometer system. The device contains several conductive rods, each comprising a conductive layer, a resistive layer, and an insulative layer between the conductive and resistive layers

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