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ProteoMonitor s IP Roundup: Recent Patents of Interest in Proteomics: Aug 26, 2005

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US Patent No. 6,933,384. Synthetic molecules for labeling histidine-rich proteins. Inventors: Roger Tsien, Christina Hauser. Assignee: The Regents of the University of California.

The invention provides Zn-chelating compounds that are molecularly engineered to bind to a specific target sequence in a protein of interest. The Zn2+ ion is far less toxic and promiscuous than nickel and therefore provides an attractive alternative to Ni-based labeling systems. The Zn-chelating compounds also do not require oxidizable thiols and therefore can be used in non-reducing environments such as the surface of living cells. In addition, the target sequence is genetically encodable and requires incorporation of only a few amino acids, unlike fusions to fluorescent proteins such as GFP.


US Patent No. 6,933,497. Time-of-flight mass analyzer with multiple flight paths. Inventor: Marvin Vestal. Assignee: PerSeptive Biosystems.

Describes a TOF mass analyzer with multiple flight paths that includes a pulsed ion source generating a packet of ions and accelerating it. An ion deflector directs a first group of ions from the packet to a first ion path, and a second group of ions to a second ion path for a predetermined time interval after the pulsed ion source generates the packet of ions. A first TOF mass separator separates the first group of ions according to their mass-to-charge ratio and a first detector is positioned to receive the first group of ions. A second TOF mass separator separates a second group of ions according to their mass-to-charge ratio and a second detector is positioned to receive the second group of ions. Additional ion paths may be employed, and any type of TOF mass separator may be used in each ion path.


US Patent No. 6,932,895. Automated electrophoresis gel manipulation apparatus. Inventors: Leigh Anderson, Jack Goodman, Eric Wallgren. Assignee: Large Scale Proteomics.

Describes an automated, computer controlled assembly for continuously processing a large number of electrophoresis gels. The assembly includes a loading assembly for loading a gel onto a carrier, a gel staining assembly, and a scanning and cutting assembly. The staining assembly and the scanning and cutting assembly each include a robotic arm that is able to capture a gel and transfer the gel to selected work stations and can transfer the gel between the respective robotic arms.


US Patent No. 6,933,136. Method for making recombinant proteins. Inventors: Ruth Simesen, Anette Pedersen, Steffen Faisst, Jan Jensen, Dietmar Weilguny. Assignee: Novo Nordisk.

The invention provides nucleic acid molecules and vector constructs comprising scaffold and matrix attachment regions and methods of using such attachment regions for the industrial production of recombinant proteins and polypeptides. The invention is based on the discovery of new S/MAR elements from hamster-derived CHO and BHK cells, which may be used for increasing and stabilizing the expression yield of recombinant proteins in mammalian cells.


US Patent No. 6,931,325. Three dimensional protein mapping. Inventors: Daniel Wall, David Lubman, Timothy Barder. Assignee: Regents of the University of Michigan.

The invention relates to multi-phase protein separation methods capable of resolving and characterizing large numbers of cellular proteins, including methods for efficiently facilitating the transfer of protein samples between separation phases. In particular, the invention provides systems and methods for the generation of multi-dimensional protein maps, thus providing improved methods for the analysis of samples containing large numbers of proteins.


US Patent No. 6,925,389. Process for discriminating between biological states based on hidden patterns from biological data. Inventors: Ben Hitt, Emanuel Petricoin, Peter Levine, Lance Liotta. Assignee: Correlogic Systems.

The invention comprises the use of pattern discovery methods and algorithms to detect subtle, if not totally hidden, patterns in the expression of certain molecules in biological samples that are potentially diagnostic in nature, or predictive of a biological state. In one embodiment of the invention such patterns are patterns of protein expression, particularly patterns of low molecular weight proteins (i.e. less than 20,000 Da). The invention is based, in part, on the unexpectedness or non-obvious discovery of finding hidden contextual diagnostic patterns to yield a classification, e.g., the diagnosis of malignancy in cancers such as carcinomas, melanomas, lymphomas, sarcomas, blastomas, leukemias, myelomas, and neural tumors.


US Patent No. 6,921,642. Protein expression profiling. Inventors: Stephen Kingsmore, Girish Nallur, Barry Schweitzer. Assignee: Qiagen.

This patent protects compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. The amplified DNA serves as a readily detectable signal for the proteins. The method can also be used to compare the proteins expressed in two or more different samples and allows sensitive and accurate detection and quantitation of proteins expressed in any cell or tissue.


US Patent No. 6,921,638. Hydrogel-based microarray signal amplification methods and devices therefore. Inventors: Chang-Gong Liu, Abhijit Mazumder, Charles Brush, Travis Johnson. Assignee: Amersham Biosciences.

The invention provides methods and devices for detecting nucleic acid and protein targets on hydrogel microarrays. Fluorophores are incorporated into the targets and detected. A linear correlation between target concentration and signal amplitude is maintained through the elimination of active enzyme amplification.


US Patent No. 6,906,320. Mass spectrometry data analysis techniques. Inventors: Jeffrey Sachs, Matthew Wiener, Nathan Yates. Assignee: Merck.

The invention features mass spectrometry data analysis techniques that can be employed to selectively identify analytes differing in abundance between different sample sets. The techniques determine the statistical significance of changes to signals associated with mass-to-charge ratios ("m/z-intensity pairs") between individual samples and sample sets. Based on the statistical significance, changes likely to indicate analyte level differences are identified. Based on intensities of the signals, ratios of analyte abundances can be determined.


US Patent No. 6,914,239. System for analyzing mass spectrometric data. Inventors: Kiyomi Yoshinari, Kinya Kobayashi, Atsushi Otake, Toyoharu Okumoto. Assignee: Hitachi.

The object of the invention is to make it feasible to identify a parent ion or its estimate structure accurately, by utilizing mass spectrometric data MS.sup.N (N?3) for which a database is not available. The invention is able not only to provide structure of a parent ion and dissociated ions accurately but also to display it by executing molecular orbital analysis and molecular dynamic calculation for mass spectrometric data (MS data, MS.sup.2 data and MS.sup.N data N?3), which is obtained by multiple-stage dissociation of the parent ion.


US Patent No. 6,913,886. Fast and exhaustive method for selecting a prey polypeptide interacting with a bait polypeptide of interest: application to the construction of maps of interactors polypeptides. Inventors: Pierre Legrain, Micheline Fromont, Jean-Christophe Rain. Assignee: Institut Pasteur.

The aim of the invention is to provide a new method for selecting a polynucleotide encoding a prey polypeptide in a two-hybrid screening system. It makes use of mating recombinant haploid yeast cells instead of recombinant yeast cell colonies, providing significant advantages over prior art.


US Patent No. 6,932,845. Method for performing submicroliter crystallization experiments. Inventors: Bernard Santarsiero, Raymond Stevens, Peter Schultz, Joseph Jaklevic, Derek Yegian, Earl Cornell, Roberd Nordmeyer. Assignee: The Regents of the University of California.

The invention relates to methods and apparatuses for crystallizing molecules and, more particularly, for automating the crystallization of molecules, especially macromolecules such as proteins. It describes a method for performing array microcrystallizations to determine suitable crystallization conditions.


US Patent No. 6,911,056. Method for diffracting crystals formed by submicroliter crystallization experiments. Inventors: Bernard Santarsiero, Raymond Stevens, Peter Schultz, Joseph Jaklevic, Derek Yegian, Earl Cornell, Robert Nordmeyer. Assignee: The Regents of the University of California.

The invention relates to methods and apparatuses for crystallizing molecules, in particular for automating the crystallization of macromolecules such as proteins. It provides a method for performing array microcrystallizations to determine suitable crystallization conditions.


US Patent No. 6,908,740. Methods and apparatus for gel-free qualitative and quantitative proteome analysis, and uses therefore. Inventors: Joel Vandekerckhove, Kris Gevaert.

Provides methods and apparatus for qualitative and quantitative proteome analysis. These allow for the isolation of a subset of peptides out of complex mixtures of peptides. The isolation is based on a specific chemical and/or enzymatic alteration of one or more types of peptides. This alteration modifies the biophysical, chemical,l or any other biochemical property of the affected types of peptides (e.g., net electrical charge and/or hydrophobicity) in such way that the altered peptides can be separated from the unaltered peptides.


US Patent No. 6,906,319. Mass Spectrometer. Inventor: John Hoyes. Assignee: Micromass.

Patent protects a mass spectrometer where ions with a particular desired charge state are selected by operating an ion mobility spectrometer in combination with a quadrupole mass filter. Precursor ions are fragmented or reacted to form product ions in a collision cell ion trap and sent back upstream to an upstream ion trap. The fragment or product ions are then passed through the ion mobility spectrometer wherein they become temporally separated according to their ion mobility. Fragment or product ions are then re-trapped in the collision cell ion trap before being released in packets. A pusher electrode of a time of flight mass analyzer is energized a predetermined period of time after a packet of ions is released from the collision cell ion trap. Accordingly, it is possible to select multiply charged precursor ions from a background of singly charged ions, fragment them, and mass analyze the fragment ions with a near 100% duty cycle across the whole mass range.


US Patent No. 6,905,879. Isotope-coded ionization-enhancing reagents (ICIER) for high-throughput protein identification and quantitation using matrix-assisted laser desorption ionization mass spectrometry. Inventors: Yongchang Qiu, Jack Wang, Rodney Hewick. Assignee: Genetics Institute.

Provides arginine-containing cysteine-modifying compounds useful for MALDI-MS analysis of proteins. These compounds, termed isotope-coded ionization enhancement reagents (ICIER), can provide ionization enhancement in MALDI-MS, relative quantitation, and additional database searching constraints at the same time without any extra sample manipulation. More specifically, ICIER increase the ionization efficiency of cysteine-containing peptides by attachment of a guanidino functional group. ICIER also increase the overall hydrophilicity of these peptides due to the hydrophilic nature of ICIER and thus increase the percentage of recovery of these peptides during sample handling and processing such as in-gel digestion or liquid chromatography. Finally, a combination of both light and heavy ICIER provides an accurate way to obtain relative quantitation of proteins by MALDI-MS and additional database searching constraints (number of cysteine residues in every single peptide peak) to increase the confidence of protein identification by peptide mass mapping.


US Patent No. 6,905,584. Electrophoresis system and method therefore. Inventor: Ben Herbert. Assignee: Proteome Systems.

The idea of the invention is to propose a novel method for allowing a first dimension isoelectric focusing gel and a second dimension electrophoresis gel to be combined, stored, shipped and run in a single cassette which is susceptible to automation. Describes a method for separating a sample into components by two-dimensional electrophoresis uses an IPG strip, and a gel slab which are spaced apart and carried on a single generally planar support means.


US Patent No. 6,902,936. Acid-labile isotope-coded extractant (ALICE) and its use in quantitative mass spectrometric analysis of protein mixtures. Inventors: Yongchang Qiu, Jack Wang, Rodney Hewick. Assignee: Genetics Institute.

The method of the invention provides novel compounds, termed acid-labile isotope-coded extractants (ALICE), for quantitative mass spectrometric analysis of protein mixtures. The compounds contain a thiol-reactive group that is used to capture cysteine-containing peptides from all peptide mixtures, an acid-labile linker, and a non-biological polymer. One of the two acid-labile linkers is isotopically labeled and therefore enables the direct quantitation of peptides/proteins through mass spectrometric analysis. In combination with our novel dual column two dimensional liquid chromatography-mass spectrometry (2D-LC-MS/MS) design, the ALICE procedure proves to be a general approach for quantitative mass spectrometric analysis of protein mixtures with better dynamic range and sensitivity.


US Patent No. 6,911,311. Method of detecting protein-protein interactions. Inventor: John Manfredi. Assignee: Myriad Genetics.

This invention provides a versatile and sensitive in vitro assay system for detecting protein-protein interactions and for selecting compounds capable of modulating protein-protein interactions. Particularly, the present invention utilizes the so-called inteins, which are peptide sequences capable of directing protein trans-splicing in vitro. An intein is an intervening protein sequence in a protein precursor that is excised from the protein precursor during protein splicing. Protein splicing results in the concomitant ligation of the flanking protein fragments, i.e., the exteins, with a native peptide bond, thus forming a mature extein protein and the free intein. It is now known that inteins incorporated into non-native precursors can also cause protein-splicing and excision of the inteins.


US Patent No. 6,913,701. Method for fabricating integrated LC/ESI device using SMILE, latent masking, and delayed LOCOS techniques. Inventors: James Moon, Timothy Davis, Gregory Galvin, Kevin Shaw, Paul Waldrop, Sharlene Wilson. Assignee: Kionix.

The invention relates to the design, development, and manufacturing of miniaturized chemical analysis devices and systems using microelectromechanical systems (MEMS) technology. In particular, the invention relates to improvements in process sequences for fabricating MEMS and microfluidic devices, including electrospray ionization, liquid chromatography, and integrated liquid chromatography/electrospray devices.


US Patent No. 6,903,334. High throughput ion source for MALDI mass spectrometry. Alexander Makarov, Anatoli Verentchikov. Assignee: Thermo Finnigan.

The invention provides methods and apparatus, including ion sources and mass spectrometers incorporating such ion sources, for high throughput mass analysis. The methods and apparatus, some of which are particularly applicable for applications in the area of genomics and proteomics, are based on MALDI at intermediate gas pressure with a high repetition rate and high-energy laser beam. The proposed apparatus incorporates matrix-protecting interfaces configured so that the shortest travel path between an illuminated portion of the sample plate and the input to ion optics, or an ion sampling aperture, is substantially obstructed and/or so that contaminating particles are repelled away from the matrix-protecting interface, e.g., by gas flow, while an electric field extracts analyte ions of interest.