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Recent Patents of Interest in Proteomics: Jul 3, 2008

US Patent 7,395,160. Quality assurance/quality control for electrospray ionization processes. Inventors: Ben Hitt; Peter Levine; Timothy Coleman. Assignee: Correlogic Systems
A method is described for high-throughput bioassay processes that include generating a bioassay process model and comparing spectral data based on a combination of a biochip and a test serum to the bioassay process model to determine if the test sample and bioassay process are producing acceptable data.

US Patent 7,393,918. Protein binding miniature proteins and uses thereof. Inventors: Dasantila Golemi-Kotra; Alanna Schepartz Shrader. Assignee: Yale University
Invention pertains to miniature proteins resulting from a protein scaffold “such as an avian pancreatic polypeptide that can be modified by substitution of at least one amino acid residue,” according to the patent’s abstract. In other aspects the invention provides diagnostic and therapeutic uses for the miniature proteins.

US Patent 7,391,017. Mass scale alignment of time-of-flight mass spectra. Inventors: Markus Kostrzewa; Stefan Klepel Thomas Maier. Assignee: Bruker Daltonik
The invention generates mass scale comparability between mass spectra acquired in TOF mass spectrometers, particularly with ionization by MALDI. After alignment of the mass scales, mass spectra can be “reliably compared with respect to deviations in intensities of [biomarkers], or be added together without deterioration in the mass resolution, and improved reference spectrum libraries can be created,” according to the patent’s abstract.

US Patent 7,390,640. Circular permutant GFP insertion folding reporters. Inventors: Geoffrey Waldo; Stephanie Cabantous. Assignee: Los Alamos National Security
Described are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including those of GFP variants and combinations thereof. Also provided are nucleic acid molecules and vectors incorporating such nucleic acid molecules “comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP,” the authors say in the patent’s abstract.

US Patent 7,390,639. Staphylococcal nuclease fusion proteins for the production of recombinant peptides. Inventors: Zhengding Su; Feng Ni. Assignee: National Research Council of Canada
The carrier proteins disclosed in the patents are adapted from the N-terminal domain of Staphylococcus nuclease, which acts to promote the over-expression of the peptide-protein fusion in the form of inclusion bodies. The process minimizes in-cell proteolysis of desired peptides. In addition to high yields, the method described can be used for producing isotopically labeled peptides for NMR characterization of bioactive peptides and their interactions with target proteins.

US Patent 7,390,463. Microcolumn-based, high-throughput microfluidic device. Inventors: Lin He; Jinlin Peng; Youchun Shi; Brian Webb; Po Ki Yuen. Assignee: Corning
Patent pertains to an assay device. The invention includes a fluidic or microfluidic device, which integrates fluidic capability into “existing multi-well plates of standard configuration, for performing either single or continuous fluidic manipulations in a high-throughout format,” according to the patent’s abstract.

US Patent 7,388,197. Multiplex data acquisition modes for ion mobility-mass spectrometry. Inventors: John McLean; David Russell; Thomas Egan; Michael Ugarov; J.A. Schultz. Assignee: Ionwerks
Described is a method and apparatus for multiplexed acquisition for gas-phase ion mobility coupled with mass spectrometry. Ion packets are injected into an ion mobility drift chamber at a rate faster than the ion mobility separation arrival time distribution.

US Patent 7,388,195. Apparatus and systems for processing samples for analysis via ion mobility spectrometry. Inventors: Angela Zapata; Ernest Kim; Priya Agrawal; Melissa Krebs; Cristina Davis. Assignee: Charles Stark Draper Laboratory
Invention pertains to an assembly for delivering an ionized analyte from an ionization apparatus into an ion mobility spectrometer, allowing for analysis of biological and non-biological samples. Provided are also portable sample analysis systems that operate at ambient pressure.

US Patent 7,385,186. Methods of operating ion optics for mass spectrometry. Inventors: Kevin Hayden; Marvin Vestal. Assignee: Applera [now called Applied Biosystems]; MDS
Methods are described for focusing ions for an ion fragmentor and for operating an ion optics assembly. In various embodiments, the methods “substantially maintain the position of the focal point of the an incoming ion beam over a wide range of collision energies, and thereby provide a collimated ion beam for a collision cell over a wide range of energies,” according to the patent’s abstract.

US Patent 7,384,794. Micro-devices and analytical procedures for investigation of biological systems. Inventor: Janusz Pawliszyn. Assignee: N/A
Patent pertains to fibers with an extraction phase “coated thereon in combination with a positioning device,” which are used to perform adsorption of components of interest from an animal or animal tissue.

US Patent 7,384,790, Method of analyzing peptide for determining C-terminal amino acid sequence. Inventors: Kenji Miyazaki; Akira Tsugita; Naoyuki Takahashi; Takuji Nabetani; Toshimasa Yamazaki; Kenichi Kamijo. Assignee: NEC
The method calls for an alkanoic acid anhydride and a perfluoroalkanoic acid, both of vapor phase, to be allowed to act on a dry sample of the peptide to be examined in a dry atmosphere at a temperature between 15 and 60 degrees centigrade. Successive formation of a 5-oxazolone structure followed by cleavage of the 5-oxazolone ring results in the release of C-terminal amino acid. The C-terminal amino acids sequence is identified by analysis based on the decrease in molecular weight in a series of the reaction products obtained.

US Patent 7,384,754. Enrichment and tagging of glycosylated proteins. Inventors: Karla Robotti. Assignee: Agilent Technologies
A method is described in which a mixture containing glycosylated and unglycosylated proteins is contacted with a resin that includes a nucleophile bound to a solid support via a linker. The contacting is done under conditions resulting in the removal of the glycosyl group from the glycosylated proteins and to “concomitantly result in the deglycosylated proteins covalently bound to the solid support,” according to the patent’s abstract.

US Patent 7,381,373. System and method for preparative mass spectrometry. Inventors: Thomas Blake; Zheng Ouyang; Robert Cooks. Assignee: Purdue Research Foundation
The preparative MS system includes an ionizer which converts the mixture into gas phase ions of the molecules in the mixture. It also has a separator that separates the ions according to their mass-to-charge ratio or mobility.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.