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Recent Patents of Interest in Proteomics: Jan 15, 2010


US Patent 7,642,509. Top-down protein analysis in mass spectrometers with ion traps. Inventors: Ralf Hartmer; Jochen Franzen. Assignee: Bruker Daltonik

Proteins with a molecular mass of between 5 and 100 kiloDaltons are structurally analyzed without prior enzymatic digestion to small peptides in a mass spectrometer operating with an ion trap. Electrospraying or other similar processes ionize the proteins to create highly charged ions. These are then introduced into the ion trap and subjected to fragmentation and partial deprotonation. An evenly distributed mixture of fragment ions having between one and at about three to eight charges is left in the ion trap. "A mass spectrum is recorded from this mixture of fragment ions, which spectrum demonstrates a sequence coverage that far exceeds the mass range of the mass analyzer for singly charged ions," according to the abstract.

US Patent 7,342,089. Immunosubtraction method. Inventors: Rembert Pieper; Leigh N. Anderson. Assignee: Agilent Technologies

Pertains to the removal of abundant proteins from samples. This is done by immunosubtraction of "several high abundance, interfering, or contaminating proteins simultaneously," according to the abstract.

US Patent 7,642,085. Protein arrays. Inventors: Peter G. Schultz; Lei Wang. Assignee: The Scripps Research Institute

Provided are proteins attached to solid supports and methods to devise such solid-support proteins. An unnatural amino acid incorporated into the protein attaches the proteins to the solid supports.

US Patent 7,641,780. Two-dimensional microfluidics for protein separations and gene analysis. Inventors: Cheng Sheng Lee; Don DeVoe. Assignees: Calibrant Systems; University of Maryland

Provided is a microfluidic device for performing 2D biomolecular separations. The device "may include first and second planar substrates, which include at least a first dimension microchannel extending in a first direction and an array of second dimension microchannels extending in a second direction, preferably, orthogonal to the first dimension," according to the abstract. Some of the ends of the microchannels are in fluid communication with a several reservoirs, and substrates may include a number of microchannels and reservoirs. The reservoirs are in communication with a number of electrodes and voltage power sources.

US Patent 7,641,778. Gel electroelution and sample separation devices and associated processes. Inventors: James H. Lenke; Matthew Powell. Assignee: Protea Biosciences

Covers a gel electrolelution device that can have a gel spot column with upstream and downstream openings in fluid communication with an inlet and outlet, respectively. "A gel electroelution process can involve flowing a buffer solution through the gel spot in a first direction, and creating an electric field across the gel spot in the same direction," according to the abstract.

US Patent 7,638,764. Systems and methods for reducing noise from mass spectra. Inventor: Gordana Ivosev. Assignees: MDS Analytical Technologies; Applied Biosystems

The methods covered comprise obtaining an original mass spectrum; determining a noise mass spectrum that corresponds to background noise in the original mass spectrum; and subtracting the noise mass spectrum from the original mass spectrum.

US Patent 7,635,841. Method of mass spectrometry. Inventors: Robert Harold Bateman; John Brian Hoyes; Jason Lee Wildgoose; Anthony James Gilbert. Assignee: Micromass [now called Waters]

Covers a method in which ions are trapped "for a period of time T within an AC or RF ion guide maintained at a pressure P wherein the product P times T is at least 1 mbar-ms," according to the abstract. "The effect of trapping the ions according to a preferred embodiment is that singly charged ions that may, for example, comprise unwanted background ions, are substantially lost from the trap whereas multiply charged analyte ions are maintained within the ion trap and can then be released for subsequent mass analysis," the inventors said in the abstract.

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US Patent 7,635,573. Mass spectroscopic method for comparing protein levels in two or more samples. Inventor: Steven M. Fischer. Assignee: Agilent Technologies

Pertains to a method for quantitative determination and/or identification of proteins in a sample. In one aspect, mass spectrometry is used to compare protein levels in two or more samples by differentially isotopically labeling each sample's proteins N- or C-termini. In another aspect, a mass spec-based method is provided for identifying a sample as a source for a protein from a mixture of two or more samples by differentially isotopically labeling each sample's proteins' N- or C-termini.

US Patent 7,635,572. Methods for conducting assays for enzyme activity on protein microarrays. Inventors: Fang X. Zhou; Barry Schweitzer. Assignee: Life Technologies

Pertains to methods of "conducting assays for enzymatic activity on microarrays useful for the large-scale study of protein function, screening assays, and high-throughput analysis of enzymatic reactions," according to the abstract. Methods are described for using protein chips to assay the presence, amount, activity, and/or function of enzymes present in a protein sample or protein chip.

US Patent 7,635,425. Integrated high-throughput system for the analysis of biomolecules. Inventors: Kemmons A. Tubbs; Karl F Gruber; Randall W. Nelson. Assignee: Intrinsic Bioprobes

The system consists of an affinity microcolumn "comprising a high surface area material, which has high flow properties and a low dead volume, contained within a housing and having affinity reagents bound to the surface of the high surface area material that are either activated or activatable," according to the abstract.

US Patent 7,632,686. High sensitivity quantitation of peptides by mass spectrometry. Inventor: Norman L. Anderson. Assignee: Anderson Forschung Group

Provided is an economical flow-through method for determining the amount of proteins in a sample. An antibody preparation is used to capture a specific monitor peptide and an internal standard peptide and enrich them. Upon elution into a mass spec, the sample-derived peptide and internal standard peptide are quantitated. Their measured abundance ratio is used to calculate the abundance of the monitor peptide and its parent protein in the initial sample.

US Patent 7,629,744. In-gel tagging and in-gel digestion for phosphoproteins analysis and phosphorylation site identification. Inventors: Yeong Hee Ahn; Jong Shin Yoo; Jae Young Lee; Jin Young Kim; Kun Cho. Assignee: Korea Basic Science Institute

Covers a method for phosphorylation site-specific labeling of phosphoproteome with a site-specific tagging reagent and analysis. In particular, it pertains to a method of "in situ tagging of phosphorylation sites of phosphoproteins retained in polymeric gel with a nucleophilic tagging reagent," according to the abstract. A method for generating new proteolytic cleavable sites at former phosphorylation sites "by a proper choice of nucleophilic tagging reagent," is also described. "The invention provides in-gel chemical tagging method for phosphoaminoacid residue of phosphoproteins retained in polymeric gel matrix," according to the abstract.

US patent 7,628,914. Methods for time-alignment of liquid chromatography-mass spectrometry data. Inventor: Scott M. Norton. Assignee: PPD Biomarker Discovery Sciences

"Nonlinear retention time variations in chromatography-mass spectrometry data sets are adjusted by time-alignment methods, enabling automated comparison of spectra for differential phenotyping and other applications," according to the abstract.

US Patent 7,622,712. Method for operating an ion trap mass spectrometer system. Inventor: James Hager. Assignee: MDS Analytical Technologies; Applied Biosystems

The method comprises "encoding a selected characteristic in at least one of the first group of precursor ions and the first plurality of fragments, wherein the encoding operation is applied to at least one of the first group of precursor ions and the first plurality of fragments without being applied to other ions such that the first plurality of fragment ions has the first selected characteristic and the other ions lack the first selected characteristic," according to the abstract.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.