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Recent Patents of Interest in Proteomics: Sep 24, 2010


US Patent No. 7,800,058. Mass spectrometer and mass spectrometry method. Inventors: Masuyuki Sugiyama, Yuichiro Hashimoto, Hideki Hasegawa, Izumi Waki. Assignee: Hitachi High-Technologies.

Describes a mass spectrometer that can operate as either a linear trap or as a mass filter, and can attain both high ejection efficiency when operated as a linear trap and high mass resolving power when operated as a mass filter. The mass spectrometer includes an ion source for ionizing a sample, a linear trap quadrupole rod lens with ionized ions, a trap electrode for forming a potential to trap the supplied ions between one end of the quadrupole lens and the other end, a control unit to regulate the trap lens voltage, and a mass analyzer or detector to detect ions ejected from the linear trap. The mass spectrometer is characterized by "switching between an operation where the supplied ions are trapped in a section quadrupole rod lens and ejected by the controller unit regulating the trap electrode voltage, and an operation where ions are selective passed through according to their mass," according to the patent abstract. "The ejection efficiency when operated as an ion trap, and the mass resolving power when operated as a quadrupole mass filter are vastly improved compared to conventional methods," the abstract states.

US Patent No. 7,800,055. System and method for grouping precursor and fragment ions using selected ion chromatograms. Inventors: Scott Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein. Assignee: Waters Technologies.

Covers the analysis of LC/MS data to determine groupings of ions associated with originating molecules. After initial groupings of ions are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.

US Patent No. 7,799,576. Isobaric labels for mass spectrometric analysis of peptides and method thereof. Inventors: Darryl Pappin, Michael Bartlet-Jones. Assignee: DH Technologies Development.

Protects methods, mixtures, kits and/or compositions for determining analytes by mass analysis "using unique labeling reagents or sets of unique labeling reagents," according to the patent abstract. The labeling reagents can be isomeric or isobaric and can be used to produce mixtures suitable for multiplex analysis of the labeled analytes.

US Patent No. 7,799,570. Methods for validating the presence of and characterizing proteins deposited onto an array. Inventor: Daniel Schabacker. Assignee: University of Chicago, Argonne National Laboratory.

Describes a method of determining if proteins have been transferred from liquid-phase protein fractions to an array. The method comprises first staining the array with a protein stain and then imaging the array in order to compare the staining with a standard curve generated by staining known amounts of a known protein on the same or a similar array. The patent also protects a method of characterizing proteins transferred from liquid-phase protein fractions to an array that includes staining the array with a post-translational modification-specific stain, imaging the array, washing the array, re-staining the array with a total protein stain, imaging the array, and comparing the imaging of the PTM-specific stain with the imaging of the total protein stain.

US Patent No. 7,799,526. Phosphoprotein detection reagent and methods of making and using the same. Inventor: Alan Howe. Assignee: The University of North Carolina at Chapel Hill.

Discloses a phosphoprotein detection reagent that selectively binds phosphoamino acids. The patent provides methods of generating and employing the reagent, methods of detecting modulation of protein phosphorylation, methods of detecting a change in state of a cell, as well as a kit for the detection of phosphoproteins.

US Patent No. 7,799,519. Diagnosing and grading gliomas using a proteomics approach. Inventor: Richard Caprioli. Assignee: Vanderbilt University.

Protects a proteomic approach to grading gliomas and for predicting patient survival. "In addition to employing global protein expression patterns, such as by mass spectrometry, particular target proteins whose expression is altered in various gliomas can be used to predict the stage/classification of a glioma, as well as to indicate whether a given patient will be a short- or long-term survivor," the patent's abstract states.

US Patent No. 7,797,988. Liquid chromatography-mass spectrometry. Inventors: Gary Schultz, Reinaldo Rodrigo Queiros de Almeida, Mark Haydn Allen. Assignee: Advion BioSystems

Covers an LC/MS system that includes "a chromatographic column through which an effluent passes, wherein the effluent comprises a plurality of analytes that correspond to a plurality of chromatographic peaks and an eluent, a post-column splitter having at least two output ports through which the effluent of the column is split to at least a first portion and a second portion, a mass spectrometer configured to receive the first portion from a first of the output ports for analysis, and a tube connected to a second of the output ports configured to prevent substantial evaporation of the eluent in the second portion until undergoing mass spectrometry."

US Patent No. 7,795,405. Procedure for the fractionation of proteins by using sequential ion exchange and hydrophobic interaction chromatography as prefractionation steps before analysis by two dimensional electrophoresis. Inventor: Augustine DiNovo. Assignee: Guild Associates.

Discloses devices, systems, and methods for proteomic fractionation "that may increase the number of protein spots visualized by 2DE analysis, and may allow enrichment of proteins normally not detectable by standard 2DE analysis," according to the patent abstract. Devices, systems, and methods of the disclosure relate to fractionating a proteome on the basis of surface charge, hydrophobicity, isoelectric point, and/or size.

US Patent No. 7,795,010. Fractionator and method of fractionation. Inventors: Kazuhiro Tanahashi, Ichiro Kumo, Nobuyuki Kuroki, Hiroyuki Sugaya, Satoko Yamada, Shigehisa Wada, Giman Jung, Toshihiko Kuroda, Shuji Sekiguchi. Assignee: Toray Industries.

Discloses a membrane fractionator that includes a filtration section, a concentrating section, a recovery section, and a liquid feed pump, wherein a flow channel connecting the filtration section, concentrating section, and recovery section constitutes a closed circuitry. The patent also discloses a method of biocomponent separation in which a sample derived from biocomponents is fed into an antibody-adsorption membrane-separation system. The patent also covers a method of protein fractionation that includes bringing a solution containing two or more types of proteins and water into contact with a hollow yarn separation membrane "to thereby attain protein fractionation, characterized in that the fractionation solution contains an organic solvent," the patent abstract states.

US Patent No. 7,794,964. Biochip for the detection of phosphorylation and the detection method using the same. Inventors: Sang-Hyun Park, Kyong Cheol Ko. Assignee: Korea Atomic Energy Research Institute.

Protects a biochip and a method for detecting phosphorylation using the biochip. The biochip is prepared by integrating a protein produced from the recombination of a substrate of a protein kinase with an elevated protein, such as Selenomonas ruminantium membrane protein, on a matrix surface coated with an active group. A kit for detecting phosphorylation is composed of the biochip and a cofactor labeled with a radio-isotope. The biochip "facilitates the detection of phosphorylation with a minimum amount of a sample by simple processes, compared with the conventional method using an antibody," according to the patent abstract. "Since this method can analyze a large amount of samples in a shorter period of time, it can be effectively used for the analysis of kinase activity."

US Patent No. 7,794,952. Biomarker isolation and use thereof to characterize physiological state. Inventors: Lance Liotta, Emanuel Petricoin. Assignee: George Mason University.

Relates to compositions and methods for characterizing the physiological state of a living system that involves capturing biomarkers from the living system and then correlating their presence or absence to a physiological state. In one embodiment, the invention relates to a method of detecting a polypeptide biomarker in a blood serum or plasma sample obtained with an affinity ligand that is capable of binding to different polypeptide biomarkers derived from the same parental molecule.

US Patent No. 7,794,947. Affinity capture of peptides by microarray and related methods. Inventors: Rudolf Aebersold, Hui Zhang. Assignee: Institute for Systems Biology.

Describes methods of detecting polypeptides in a sample that can include the steps of cleaving polypeptides in a test sample to generate peptides, adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards, washing the array to remove unbound peptides, and determining the presence of bound test peptides and standard peptides.

US Patent No. 7,785,649. Method for manufacturing protein chip substrate using plasma and protein chip substrate manufactured by the method. Inventors: Dong-geun Jung, Sang-hak Yeo, Chang-rok Choi. Assignee: Sungkyunkwan University Foundation for Corporate Collaboration.

Discloses a protein chip substrate and a method for manufacturing the protein chip substrate. The method includes deposition of plasma polymerized ethylenediamine with an amine group on plasma polymerized cyclohexnane by inductively coupled plasma-chemical vapor deposition, "thereby preventing non-specific adsorption of proteins on a slide surface," the patent abstract states.

US Patent No. 7,783,429. Peptide sequencing from peptide fragmentation mass spectra. Inventors: Peter Walden, Rodion Demine. Assignee: Charite'-Universitatsmedizin Berlin.

Covers a method of peptide sequencing from peptide fragment mass data that includes calculating peptide fragment masses, searching peak data for masses matching the calculated peptide fragment masses, annotating all permutations of the peak data with amino acid sequences that correspond to the calculated peptide fragment masses, extending the potential sequences to resulting masses with additional matching masses, extending stepwise additions "until the resulting masses correspond to parental peptide masses or said parental peptide masses minus the mass of water," and identifying at least one peptide sequence by deleting sequences that can not be extended to endpoints of the parental peptide masses.

US Patent No. 7,781,729. Analyzing mass spectral data. Inventors: Yongdong Wang, Ming Gu. Assignee: Cerno Bioscience.

Protects a method for analyzing data from a mass spectrometer that includes processing raw spectral data, obtaining library spectral data that has been processed to form calibrated library data, and performing a least-squares fit between the calibrated continuum spectral data and the calibrated library data to determine concentrations of components in a sample that generated the raw spectral data.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.