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Recent Patents of Interest in Proteomics: Dec 11, 2008

US Patent 7,462,494. Method for laser desorption mass spectrometry using porous polymeric substrates with particle fillers. Inventors: Brinda Lakshmi; Bathsheba Chong Conklin. Assignee: 3M Innovative Properties
Invention pertains to articles and methods for the high-energy desorption/ionization of various compositions. The methods use porous substrates, “optionally in combination with one or more surface coatings and fillers,” to provide enhanced desorption of analytes, according to the abstract.

US Patent 7,462,489. Methods of identifying and analyzing biomarkers from plasma-derived microparticles. Inventors: Klaus Ley; David Smalley. Assignee: N/A
A method is described for identifying candidate biomarkers in the plasma microparticle proteome. Also provide are methods for isolating, identifying, and analyzing microparticles derived from plasma, particularly platelet-poor plasma.

US Patent 7,460,960. Proteome epitope tags and methods of use thereof in protein modification analysis. Inventors: Frank Lee; Xun Meng; David Livingston. Assignee: Epitome Biosystems
Methods are described for detecting proteins, particularly proteins with post-translational modifications, in a sample by using one or more capture agents that recognize and interact with recognition sequences “uniquely characteristic of a set of proteins (Proteome Epitope Tags) in the sample,” according to the patent’s abstract. Provided also are arrays comprising capture agents or PETs.

US Patent 7,459,542. Separation of albumin from protein samples. Inventors: Qing-Xiang (Amy) Sang; Ziad Joseph Sahab. Assignee: Florida State University Research Foundation
Invention pertains to methods for separating albumin from complex protein samples. The method is based on the isoelectric point of albumin and relates to forming an aqueous combination comprising the sample and an anion or cation exchange material at various pHs. This agitates the combination and separates a fraction of unbound proteins from a concentrated solids fraction made up of the ion exchange material and bound proteins.

US Patent. 7,456,276. Peptide purification by means of metal ion affinity chromatography. Inventors: Thorkild Christensen; William Hearn; Leone Spiccia; Wei Jiang; Therese Mooney; Bimbil Graham. Assignee: Novo Nordisk; Monash University
Invention pertains to a polymer substrate functionalized with a “functionality comprising at least one cyclic, metal ion coordinating ligand group, the cyclic ligand group comprising at least three metal ion coordinating donor atoms independently selected from the group consisting of nitrogen, oxygen, and sulfur,” according to the abstract.

US Patent 7,453,916. High-throughput optical micro-array reader capable of variable pitch and spot size array processing for genomics and proteomics. Inventors: Ruolin Li; Guoying Ding. Assignee: Intel
Described is an optical microarray reader system that includes microchip, VCSEL, microlens, and detector arrays. The microchip array includes multiple sample spots to be separately analyzed. The VCSEL array simultaneously illuminates more than one of the multiple spots, and the microlens array focuses optical emission from the sample spots onto the detector array.

US Patent 7,451,052. Application of comprehensive calibration to mass spectral peak analysis and molecular screening. Inventors: Yongdong Wang; Ming Gu. Assignee: Cerno Bioscience
Invention pertains to a method of performing mass spectral analysis involving at least one of the isotope satellites of at least one ion. The method comprises acquiring a measured mass spectral response including at least one of the isotope satellites and constructing a peak component matrix with mass spectral response function. It also comprises performing a regression analysis between the acquired mass spectral response and the peak component matrix, and reporting a statistical measure and regression coefficients from the regression analysis for one or more of the mass spectral peak purity assessment, ion charge determination, mass spectral deconvolution, and mass shift compensation.

US Patent 7,449,558. Site-specific labeling of proteins. Inventors: Shao Qin Yao; Su-Yin Dawn Yeo. Assignee: National University of Singapore
A method for labeling a protein having an N-terminal cysteine is described. A probe consisting of a thioester group and a detectable label is introduced into a cell expressing the N-terminal cysteine protein. This allows for the N-terminal cysteine to cleave the thioester bond, resulting in the label being covalently attached to the N-terminus of the protein by an amide bond.

US Patent 7,449,116. Methods and systems for protein separation. Inventors: James Martosella; Barry Boyes. Assignee: Agilent Technologies
Invention pertains to a system and method for protein separation. It includes fractionating a mixture of proteins on a reversed-phase superficially porous stationary phase at 40 degrees Celsius or above to recover a protein in from about 70 to 100 weight percent of the mixture of proteins.

US Patent 7,445,907. Methods for mass spectrometry detection and quantification of specific target proteins in complex biological samples. Inventors: Nicholas Everett; James Petell; Scott Young. Assignee: ISTA
Methods using mass spectrometry are described for detecting and quantifying targeted proteins in biological samples.

US Patent 7,445,894. Compostions and methods for detection and isolation of phosphorylated molecules. Inventors: Brian Agnew; Kyle Gee; Vladimir Martin. Assignee: Molecular Probes
Invention pertains to phosphate-binding compounds used for binding, detecting, and isolating phosphorylated target molecules, including molecules that interact with phosphorylated target molecules, or molecules that are capable of being phosphorylated. A binding solution is provided for use in binding and detecting immobilized and solubilized phosphorylated target molecules, isolation of phosphorylated target molecules from a complex mixture, and aiding in proteomic analysis where kinase and phosphate substrates and enzymes can be identified. 

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.