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Recent Patents of Interest in Proteomics: Oct 9, 2009

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US Patent 7,595,485. Data analysis to provide a revised data set for use in peptide sequencing determination. Inventors: Rovshan Goumbatoglu Sadygov; Andreas Huhmer. Assignee: Thermo Finnigan [now Thermo Fisher Scientific]

In one aspect, less "useful" spectral data is disregarded from the spectral data that results from fragmentation by ETD and candidate charge states for the "useful" data assigned. "Knowledge of the first order ion product charge state reduces the subset of comparison data, hence aiding in the eventual identification of the precursor ion, and thus aiding in peptide sequence database searching capabilities," according to the abstract. Such capabilities include computational requirements for database search and data storage, CPU time, and "overall improvement in the confidence in the precursor identification," the inventors said in the abstract.


US Patent 7,593,817. Calculating confidence levels for peptide and protein identification. Inventor: Fernando M Maroto. Assignee: Thermo Finnigan [now Thermo Fisher Scientific]

Pertains to computer programs and methods "for defining a misidentification probability for an experimental protein divisible into experimental peptides," according to the abstract. "The invention receives data representing a set of matches of experimental peptides to reference peptides that can be derived from a protein in a database of proteins; calculates a probability of observing by chance, in a search of the database of proteins, a set of matches equivalent to or better than the represented set of matches; and defines the misidentification probability using the probability of observing by chance a set of matches equivalent to or better than the represented set of matches."


US Patent 7,592,139. High temperature flow-through device for rapid solubilization and analysis. Inventors: Jason A West; Kyle W Hukari; Kamlesh D Patel; Kenneth A Peterson; Ronald F Renzi. Assignee: Sandia National Laboratories

Pertains to devices and methods for thermally lysing biological materials, such as vegetative bacterial cells and bacterial spores. Also, hot solution methods for solubilizing bacterial spores are described, as are systems for direct analysis, such as thermal lysers coupled to sample preparation stations. Provided are integrated systems for sample lysing, labeling and protein fingerprinting analysis of biological material.


US Patent 7,589,319. Reflector TOF with high resolution and mass accuracy for peptides and small molecules. Inventor: Marvin Vestal. Assignee: Virgin Instruments

According to the abstract, many proteomics and metabolic applications require measurements on peptides and small molecules with high resolving power and mass accuracy. Because these are often present in complex mixtures, "sensitivity over a relatively broad mass range, speed of analysis, reliability, and ease of use are very important." The invention provides "optimum performance for such applications."


US Patent 7,588,944. Method of analyzing C-terminal amino acid sequence of peptide. Inventors: Kenji Miyazaki; Akira Tsugita; Kenichi Kamijo. Assignee: NEC

An alkanoic anhydride is used to selectively and sequentially degrade an analyte peptide. "The original peptide and a series of degradation reaction products having peptide in which one or more C-terminal-sided amino acids are deleted, are subjected to a certain posttreatment," according to the abstract. Mass spectrometry is used to measure the molecular weight of the reaction products. The amino acid sequence of the original peptide from C-terminal is then determined based on the molecular weight obtained by MS.


US Patent 7,588,906. Hydrogels for biomolecule analysis and corresponding method to analyze biomolecules. Inventors: Shawn B Brueggemeier; Stephen J Kron; Sean P Palecek; Laurie Parker; Stephen Brian Henry Kent. Assignees: Wisconsin Alumni Research Foundation; University of Chicago

Described are polyacrylamide-based methods for making surface-bound peptide and protein arrays, the arrays themselves, and a method for using the arrays to detect biomolecules. Also described are methods to measure the concentration of the biomolecules, binding affinity, and kinetics. Proteins, peptides, fusion proteins, protein complexes, and nucleic acids are labeled with an acrylic moiety "and attached to acrylic-functionalized glass surfaces through a co-polymerization with acrylic monomer," according to the abstract.


US Patent 7,588,890. Device for extracting biological molecules from tissue specimens and methods for preparing the same. Inventor: Wei-Sing Chu. Assignee: N/A

Pertains to a non-destructive macromolecular extraction devise for extracting high-quality biomolecules such as proteins and DNA from tissue samples while preserving the morphology and antigenicity of the tissue.

The Scan

Removal Inquiry

The Wall Street Journal reports that US lawmakers are seeking additional information about the request to remove SARS-CoV-2 sequence data from a database run by the National Institutes of Health.

Likely to End in Spring

Free lateral flow testing for SARS-CoV-2 may end in the UK by next spring, the head of Innova Medical Group says, according to the Financial Times.

Searching for More Codes

NPR reports that the US Department of Justice has accused an insurance and a data mining company of fraud.

Genome Biology Papers on GWAS Fine-Mapping Method, COVID-19 Susceptibility, Rheumatoid Arthritis

In Genome Biology this week: integrative fine-mapping approach, analysis of locus linked to COVID-19 susceptibility and severity, and more.