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ProteoMonitor's IP Roundup: Recent Patents of Interest in Proteomics

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US Patent 6,582,965. Method for de novo peptide sequence determination. Inventors: Robert Reid Townsend, Raj Bhikhu Parekh, Sally Barbara Prime, Nick Sinclair Wedd. Assignee: Oxford GlycoSciences (now Celltech).

Covers a method for determining the amino acid sequence of an unknown peptide whose molecular mass is known. The method involves generating a virtual library of peptides with the same molecular mass as the unknown peptide, consisting of all allowed combinations of amino acids that might be present in the unknown peptide. The method involves determining a molecular mass and an experimental fragmentation spectrum for the unknown peptide, comparing its fragmentation spectrum to theoretical fragmentation spectra calculated for each member of the virtual peptide library, and then identifying a spectrum that matches the pattern most closely.


US Patent 6,586,190. Parallel high throughput method and kit. Inventors: Paul Bernasconi, Ray Donald Carpenter, Gary Keith Powell, Robert Michael Petrovich, Kimberly Ann White, Jennifer Audrey Hunt. Assignee: Syngenta Participations.

Covers a high-throughput method and kit for the discovery of small-molecule interactors of target proteins. A target module is prepared by selectively binding a target protein to a ligand that is linked to an individually detectable bead. Sets of target modules are mixed in each chamber of a multi-chamber container. Test compounds are added to each chamber, and the interaction of a compound with each target module is observed. A compound that is specific for a particular target protein will displace that protein from its target module. The identity of the disrupted target module is determined by identifying the bead to which the protein was attached.


US Patent 6,586,727. Methods and apparatus for mass spectrometry. Inventors: Robert Harold Bateman, John Brian Hoyes. Assignee: Micromass (now Waters).

Covers an improved method for parent ion scanning. In one embodiment a quadrupole mass filter upstream of a collision cell is arranged to operate in a high pass mode. Parent ions transmitted by the mass filter are fragmented in the collision cell and detected by an orthogonal time-of-flight analyzer. Ions having a mass-to-charge ratio below the cutoff of the mass filter are identified as daughter ions. In a second embodiment, the collision cell alternates between high and low fragmentation and candidate parent ions can additionally be identified on the basis of the loss of a predetermined ion or neutral particle.


US Patent 6,586,728. Variable width digital filter for time-of-flight mass spectrometry. Inventors: Edward Gavin, Leonid Braginsky. Assignee: Ciphergen Biosystems.

Provides a method and system for detecting mass-to-charge ratio of ions. A control system selects a bandwidth for filtering a signal produced by the detector. The signal is then filtered with a variable width digital filter. The bandwidth for filtering the signal may be selected from a look-up table within the control system based upon the mass-to-charge ratio of an ion of interest. Alternatively, a peak bandwidth within the signal produced by the detector may be determined and the signal may then be filtered with the variable width digital filter.


US Patent 6,590,204. Method for reducing chemical background in mass spectra. Inventor: Valdimir Baranov. Assignee: MDS.

Protects a computer-based method for reducing chemical background in acquired electrospray and nanospray mass spectra. It involves pre-processing an acquired mass spectrum, transforming it into the frequency domain, reducing peaks at calculated frequencies, applying an inverse transformation to the mass spectrum represented in the frequency domain, further processing, and subsequent output of a mass spectrum with chemical background reduced. The invention enables rapid, automated generation of mass spectra with the component attributed to chemical background reduced. It also generates mass spectra with an improved signal-to-noise ratio and sample mass accuracy.


US Patent 6,582,969. Microdevices for high-throughput screening of biomolecules. Inventors: Peter Wagner, Dana Ault-Riche, Steffen Nock, Christian Itin. Assignee: Zyomyx.

Protects methods for the parallel, in vitro screening of biomolecular activity using miniaturized microfabricated devices. The biomolecules that can be immobilized on the surface of the devices of the present invention include proteins, polypeptides, nucleic acids, polysaccharides, phospholipids, and related unnatural polymers of biological relevance. These devices are useful in high-throughput drug screening and clinical diagnostics and are preferably used for the parallel screening of families of related proteins.

 

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