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Recent Patents of Interest in Proteomics: Apr 17, 2008

US Patent 7,359,805. Methods and systems for classifying mass spectra. Inventor: Lucio Cetto. Assignee: The MathWorks
Invention pertains to methods and systems for classifying mass spectra to discriminate the absence or existence of a condition. The mass spectra may include raw mass spectrum intensity signals and intensity signals that have been preprocessed. The methods and systems include determining a first or higher-order derivative of the mass spectra signals, or a combination of the signal and derivative of the signal, to form a mass spectra data set for training a classifier.

US Patent 7,358,504. FAIMS apparatus and method for separating ions. Inventor: Roger Guevremont. Assignee: Thermo Finnigan [now Thermo Fisher Scientific]
Invention pertains to a high field asymmetric waveform ion mobility spectrometer for ion separation. A method for doing so is also described.

US Patent 7,358,052. Catalytic amplification of multiplexed assay signals. Inventor: Sharat Singh. Assignee: Monogram Biosciences
Described are methods, compositions, kits, and systems for detecting analytes in a sample. A mixture containing sample, “a first binding reagent comprising a cleavage-inducing moiety and a first binding agent specific for an analyte” and electrophoretic probes having a second binding agent is subject to conditions in which binding of respective of binding agents occur, according to the abstract.
“The interaction between the binding agents and the analyte brings the cleavage-inducing moiety within a proximity effective for cleaving a cleavable linkage tethering an electrophoretic tag to the second binding agent, thereby releasing the tag for electrophoretic separation,” according to the abstract. Different tags separate by virtue of their distinct electrophoretic mobilities. After separation, a signal amplification moiety on each tag is activated, generating a signal that indicates whether a particular analyte in the sample is present.

US Patent 7,355,010. Assay method for group transfer reactions. Inventors: Robert Lowery; Karen Kleman-Leyer; Matt Staeben; Thane Westermeyer. Assignee: BellBrook Labs
Described are methods for detecting, quantifying, and high-throughput screening of donor-products and “the catalytic activities generating the donor-products in group-transfer reactions,” according to the abstract. Immunoassays, antibodies, and kits are also provided.

US Patent 7,354,996. Method and kit for quantitative analysis of protein. Inventors: Eiichi Matsuo; Makoto Watanabe; Chikako Toda; Osamu Nishimura. Assignee: Shimadzu
Invention pertains to a method for the global quantitative analysis of protein. Method also can be applied to unpurified samples such as biological samples.

US Patent 7,354,777. Discrete nano-textured structures in biomolecular arrays, and method of use. Inventors: Mark Hart; Ho-Cheol Kim; Robert Miller; Gregor Wallraff. Assignee: International Business Machines
The biomolecular array includes a substrate “across which is distributed an array of discrete regions of a porous substance formed from a porogen-containing organosilicate material,” according to the abstract. The regions should be optically isolated from each other and can be shaped to detect optical radiation emanating from the porous substance. The discrete regions can be configured as microscopic wells within the substrate or can reside on top of the substrate in the form of microscopic mesas.

US Patent 7,354,750. Methods for separating molecules. Inventors: Daniel Simpson; Tonny Johnson; John Shultz; Roderick Flemming; Rebecca Godat; Sanchayita Kar; Robin Hurst. Assignee: Promega
Compositions and methods for separating molecules such as polypeptides and metals using a metal-modified solid support are provided. The molecules are isolated from a starting material using the modified supports of the invention. Kits used in connection to the invention’s methods are also provided.

US Patent 7,351,798. Stabilized protein crystals, formulations comprising them and methods of making them. Inventors: Alexey Margolin; Nazar Khalaf; Nancy St. Clair; Scott Rakestraw; Bhami Shenoy. Assignee: Altus Pharmaceuticals
Invention pertains to methods for stabilizing, storing, and delivering biologically active macromolecules such as proteins, peptides, and nucleic acids. Provided are methods for crystallizing proteins and preparing stabilized protein for use in dry or slurry formulations. The invention is further directed to “encapsulating proteins, glycoproteins, enzymes, antibodies, hormones, and peptide crystals, or crystal formulations into compositions for biological delivery to humans and animals,” according to the abstract.

US Patent 7,354,721. Highly sensitive proteomic analysis methods, and kits and systems for practicing same. Inventor: Grigoriy Tchaga. Assignee: Clontech Laboratories
The invention pertains to methods of determining whether a sample includes one or more analytes, particularly proteinaceous analytes. An array of binding agents is contacted with the sample. In many embodiments, contact occurs in the presence of a metal ion chelating polysaccharide, and following contact, the presence of binding complexes on the array surface are detected, and the resultant data is used to determine whether one or more analytes of interest are detected in the sample.

US Patent 7351,544. Methods to identify and quantify oligosaccharide modifications of glycoproteins. Inventor: J. Michael Pierce. Assignee: The University of Georgia Research Foundation
Invention pertains to methods for the identification of oligosaccharides found on proteins and identifying those that are modified in disease states.

US Patent 7,351,540. Protein isolation and analysis. Inventor: Francis Carr. Assignee: Merck Patent
Novel methods for identifying and sequencing proteins are provided. The methods are especially suited for screening antibody libraries. In preferred embodiments, mass spectrometry techniques are used for direct and indirect sequencing.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.