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Recent Patents of Interest in Proteomics: May 8, 2008

US Patent 7,368,290. Structural determination of intact proteins using mass spectrometry. Inventors: Gary Kruppa; Joseph Schoeniger; Malin Young. Assignee: Sandia National Laboratories
Novel methods for determining the sequence and structure of proteins are described. The invention allows for the analysis of intact proteins in a mass spectrometer, thereby eliminating the need to do sample preparation prior to introducing a protein sample to the instrument. New instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the MS, eliminating complex microseparations, and protein preparatory steps necessary for cross-linking based protein structure determination are also included.

US Patent 7,365,847. Method and apparatus for automated excision of samples from two-dimensional electrophoresis gels. Inventors: Kevin Auton; Paul Ryan; David Byatt. Assignee: N/A
Invention pertains to a system for automated excision of one or more samples from a sample media. The system described includes the use of a device for electronically capturing traits of a sample in the media and by using a microprocessor connected to the device, analyzing them by comparison to reference databases. A novel robotic excision tool is used to automatically excise and process the samples.

US Patent 7,365,312. Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis. Inventors: Julia Laskin; Jean Futrell. Assignee: Battelle Memorial Institute
Surface-induced dissociation is used in conjunction with mass spectrometric analysis for enhanced sequencing of complex molecules. “Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules,” according to the abstract.

US Patent 7,365,311. Alignment of mass spectrometry data. Inventor: Lucio Cetto. Assignee: The MathWorks
Described are methods, systems, and mediums for aligning MS data before analysis of the data is performed. The data can be received from a mass spectrometer and resampled using a smooth warping function, which can be estimated, in order to build a synthetic signal. The reference peaks may be designated by users or calculated after observing a group of spectrograms. “The synthetic signal is shifted and scaled so that the cross-correlation between the mass spectrometry data and the synthetic signal reaches its maximum value,” according to the abstract.

US Patent 7,365,310. Increased depth of field for high resolution imaging for a matrix-based ion source. Inventors: Jean-Luc Truche; Gregor Overney. Assignee: Agilent Technologies
A method is provided for producing an in-focus image of an area on a sample plate for an ion source that employs a sample plate onto which samples are deposited. The methods includes positioning an area of the sample plate in the field of view of an imaging device; producing a number of images of the area having different in-focus regions; and generating the in-focus image of the area using the plurality of images. The image may be two- or three-dimensional.

US Patent 7,365,178. Acyl-nucleotide probes and methods of their synthesis and use in proteomic analysis. Inventors: David Campbell; Marek Liyanage; Anna Szardenings; Min Wu. Assignee: Activx Biosciences
Acyl phosphase probes and methods of their preparation and use are provided. The methods and compositions can provide “enhanced simplicity and accuracy in identifying changes in the presence, amount, or activity of target proteins in a complex protein mixture, preferably nucleotide binding proteins using nucleotide binding protein-directed” tagged acyl phosphate probes, according to the abstract.

US Patent 7,364,911. Methods for isolating and labeling sample molecules. Inventors: Rudolf Aebersold; Huilin Zhou; Beate Rist; George Vella; Subhasish Purkayastha; Sasi Pillai. Assignee: N/A
A molecule is labeled by contacting a sample molecule with a solid support coupled to a chemical group comprising a cleavable functional group, one or more functional groups, and a reactive group for the sample molecule under conditions in which the sample molecule can bind covalently to the reactive group. The cleavable functional group is cleaved releasing the sample molecule, comprising the one or more functional groups, which can be a tag. A solid support covalently coupled to a chemical group is also provided.

US Patent 7,363,166. Computational method for the identification of candidate proteins useful as anti-infectives. Inventors: Samir Brahmachari; Srinivasan Ramachandran; Tannistha Nandi; Chandrika Bhimarao. Assignee: Council of Scientific & Industrial Research (India)
Invention pertains to a novel identification of candidate proteins in pathogens. The proteins may be useful as anti-infectives. It also describes a novel computational method involving calculation of sequence attributes. 

US Patent 7,361,889. Time of flight mass spectrometer. Inventor: Shinichi Yamaguchi. Assignee: Shimadzu
In the instrument described in the patent, the ions to be analyzed repeatedly fly in a loop orbit or reciprocal path. In an example of the invention, it carries out two rounds of measurement for one sample under two conditions differing in the effective flight distance of the ions to create two flight-time spectra. The data processor of the instrument compares the central points of the peaks in the two spectra to identify peaks resulting from the same kind of ion. If no peaks are identified, the data processor examines the similarity of the peak shapes to identify peaks resulting from the same kind of ion. After the correspondence of the peaks are determined, the data processor calculates the approximate m/z ratio of each ion from the difference in flight time, and calculates the number of turns of the ion based on the approximation. Using the number of turns and flight time, it calculates the exact m/z ratio.

US Patent 7,361,888. Method and apparatus for multiplexing plural ion beams to a mass spectrometer. Inventors: James Boyle; Robert Valley. Assignee: Analytica of Branford
At least two ion sources are provided with means of transporting the ions from the ion sources to separate two-dimensional ion traps. Each ion trap is used for storage and transmission of the ions. Each also operates between the ion sources and the mass analyzer. Each has a set of equally spaced parallel multipole rods and entrance and exit sections. For each ion trap, the entrance section is situated in an area where background gas pressure is at viscous flow. The pressure at the exit section “drops to molecular flow pressure regimes without a break in the structure of the ion trap,” according to the abstract. Each trap alternates stores and transmits ions “by way of a fast voltage switch applied to the ion trap exit lens,” the inventors say in the abstract.

US Patent 7,361,311. System and method for the preparation of arrays of biological or other molecules. Inventors: Robert Cooks; Zheng Ouyang. Assignee: Purdue Research Foundation
Described is a method for separating species in a mixture of molecules, particles, or atoms, then collecting the separated species. The method first converts the species in the mixture to gas phase ion by ionization. The gas phase ions are then separated based on their m/z ratio and/or mobility and collecting the separated ions. The gas phase ions are separated by filtering, or in-time or in-space and ‘soft-landed for collection such as on a surface,” according to the abstract.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.