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Recent Patents of Interest in Proteomics: Mar 27, 2008

US Patent 7,349,809. Method of non-targeted complex sample analysis. Inventor: Dayan Goodenowe. Assignee: Yol Bolsum Canada
The method involves providing a database with data of known molecules. A complex sample with multiple unidentified molecules is introduced into a Fourier Transform Ion Cyclotrom Mass Spectrometer to obtain data about the molecules in the complex sample. The molecules in the complex sample are compared to the identifying data of known molecules to identify the molecules in the sample.

US Patent 7,348,437. Proteomic analysis. Inventors: Benjamin Cravatt; Alan Saghatelian; Nadim Jessani; Arul Joseph. Assignee: The Scripps Research Institute
Described are compositions for analyzing metalloproteases. The compositions include a chemical compound including a hydroxamate moiety and a benzophenone moiety. Methods for synthesizing the compounds as well as using them for “for determining the bioactivity of compositions comprising active compounds toward a metalloprotease and for determining the potency of an inhibitor against a metalloprotease” are also provided, according to the abstract.

US Patent 7,348,416. Selective capture and enrichment of proteins expressed on the cell surface. Inventors: Bruno Domon; Ian McCaffery; Terence Ryan. Assignee: Applera
Invention pertains to a method for enriching cell surface proteins by oxidizing glycosylated protein with periodate. The method is capable of obtaining increased quantities of cell surface proteins, as well as obtaining a wide range of proteins not detectable otherwise, according to the abstract.

US Patent 7,347,922. Multi-dimensional proteomic analysis method. Inventor: Robert Akins. Assignee: N/A
The method includes the separation of proteins in one direction using cationic electrophoresis and the separation of proteins in a second orthogonal direction using other electrophoresis separation techniques. The second array may be used to determine protein-protein interactions in a sample.

US Patent 7,344,832. Method and apparatus for molecular analysis in small sample volumes. Inventors: Eric Henderson; Curtis Mosher; Janice Huff. Assignee: BioForce NanoSciences
Invention allows for the interrogation of extremely small sample volumes, according to the abstract. Probes with a plurality of domains forming a nanoarray are provided, as are methods of detecting molecule, molecular interactions, retrieving and analyzing analytes, and delivering substances to cells or tissues using probes of the invention.

US Patent 7,342,224. Obtaining tandem mass spectrometry data for multiple parent ions in an ion population. Inventors: Alexander Makarov: John Syka. Assignee: Thermo Finnigan [now Thermo Fisher Scientific]
Invention pertains to the use of a linear ion trap and time-of-flight detector to collect mass spectra to form an MS/MS experiment. The invention uses an orthogonal ejection of ions with a narrow range of m/z values to produce a “ribbon beam of ions that are injected into the collisional cell,” according to the abstract. Ions are retained in the ion trap during ejections “so that narrow ranges may be stepped through consecutively to cover all precursor ions of interest.”

US Patent 7,341,874. Method for detecting post-translational modification of peptides. Inventors: Brian Chait; Ronald Beavis; Rong Wang; Stephen Kent. Assignees: Rockefeller University; The Scripps Research Institute
Described are novel methods for identifying covalent modifications of an amino acid residue in a polypeptide chain by detecting mass differences.

US Patent 7,341,838. Polypeptides related to natriuretic peptides and methods of their classification and use. Inventors: Kenneth Buechler; Eric Fung; Tai-Tung Yip. Assignees: Biosite; Vermillion
Invention pertains to the identification and use of polypeptides that bind to antibodies directed to a desired polypeptide of interest. The inventors use natriuretic peptides and their precursors, in particular BNP, as an example and describe a number of natriuretic peptide fragments produced in biological samples that bind to antibodies directed to BNP.
According to the abstract, “Because production of such fragments is an ongoing process that may be a function of, inter alia, the elapsed time between onset of an event triggering natriuretic peptide release into the tissues and the time the sample is obtained or analyzed; the elapsed time between sample acquisition and the time the sample is analyzed; the type of tissue sample at issue; the storage conditions; the quantity of proteolytic enzymes present; etc., such fragments may be used when both designing an assay for one or more natriuretic peptides, and when performing such an assay, in order to provide an accurate prognostic or diagnostic result.”

US Patent 7,339,166. Interface and process for enhanced transmission of non-circular ion beams between stages at unequal pressure. Inventors: Keqi Tang; Alexdre Shvartsburg; Richard Smith. Assignee: Battelle Memorial Institute
Described is a new interface with non-circular conductance limit aperture. It provides an improved coupling of field asymmetric waveform ion mobility spectrometry analyzers of planar or side-to-side geometry to downstream stages such as mass spectrometry.

US Patent 7,339,036; Methods and kits for purifying his-tagged proteins. Tonny Johnson; Rebecca Godat; Laurie Engel. Assignee: Promega
Described are methods for separating a target molecule from a non-target molecule using zinc- or cobalt-charged solid supports.

US Patent 7,338,806. Reagent kit of global analysis for protein expression and method for qualitative and quantitative proteomic analysis using the same. Inventors: Shu Hui Chen; Jue Lian Hsu; Sheng Yu Huang. Assignee: National Cheng Kung University
The isotope labeling reagent is used to modify enzymatically cleaved peptides in normal or perturbed cells. MS/MS is then used to simultaneously identify protein sequence and measure the protein expression level based on variations in signal intensity.

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Combining machine learning with radiologists' interpretations further increased the diagnostic accuracy of MRIs for breast cancer, a Science Translational Medicine paper finds.

Genome Damage in Neurons Triggers Alzheimer's-Linked Inflammation

Neurons harboring increased DNA double-strand breaks activate microglia to lead to neuroinflammation like that seen in Alzheimer's disease, a new Science Advances study finds.

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.