Accuray Inc.

Cell Signaling Technology, Inc.

Other

Institute for Systems Biology

Hui Zhang

Michael Comb

Yi Tan

Dongshan Fu

Xiangming Zha

Gopinath Kuduvalli

Rudolf Hans Aebersold

John B Rush

Anton Wyss-Coray

Bai Wang

Mary Jean Tanga

Jian Luo

John Rush

Laura Ellen Downs Beaulieu

Carol Green

Rudolf H Aebersold

Compositions and methods for treatment and prevention of disorders and conditions characterized by reduced TGF-B signaling are described. In particular, the compositions and methods are useful for reducing or eliminating the pathologies associated with Alzheimer's disease. The compositions include urea derivatives containing a piperidine, piperidinium, or a piperidin-4-yl methyl; cycloalkyl, aryl, and fluorobenzyl moieties.

Benzyl urea derivatives for activating TGF-beta signaling

The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS-MS), and/or MSanalysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide. Also provided are an immunoaffinity isolation device comprising a modification-specific antibody, and antibodies against novel UFD1 and PTN6 phosphorylation sites.

Immunoaffinity isolation of modified peptides from complex mixtures

A system, method and apparatus for subtracting a synthetically-generated image, including a segmented anatomical feature, from an acquired image.

Subtraction of a segmented anatomical feature from an acquired image

A technique for generating DRR (digitally reconstructed radiography) images includes dividing sample points along a ray trajectory through a 3-dimensional dataset of attenuation values into stages. Each of the stages includes a plurality of the sample points. The attenuation values are summed along the ray trajectory for each of the sample points. Intermediate summation values are computed for each of the stages along the ray trajectory and for each of the stages the attenuation values summed within a given stage are summed with a previous stage intermediate summation value calculated for a stage previous to the given stage to generate a given stage intermediate summation value. A final accumulation value being representative of a total attenuation summed along the ray trajectory is calculated.

High quality volume rendering with graphics processing unit

The invention provides methods of detecting polypeptides in a sample. The method can include the steps of cleaving polypeptides in a test sample to generate peptides; adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, wherein the peptide standards correspond to peptides cleaved with the same reagent used to cleave the test sample; contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards; washing the array to remove unbound peptides, thereby retaining affinity captured sample peptides and standard peptides; analyzing the affinity captured peptides using mass spectrometry; and determining the presence of bound test peptides and standard peptides. The method can further include the step of quantifying the amount of the test peptides by comparing the ratio of test peptide to corresponding standard peptide.

Affinity capture of peptides by microarray and related methods

A method and apparatus for tracking a pathological anatomy within a patient's body is described. A data model of a skin surface of the patient's body may be acquired using light reflected from the skin surface. The data model can be matched with skin surfaces reconstructed and/or interpolated from four-dimensional (4D) diagnostic imaging data, such as 4D CT data, to determine a temporal phase of the patient's respiratory motion. The identified temporal phase may then be used in conjunction with the diagnostic imaging data to identify a location of the pathological anatomy within the patient's body.

Target tracking using surface scanner and four-dimensional diagnostic imaging data

The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS&#x2014;MS), and/or MSanalysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide. Also provided are an immunoaffinity isolation device comprising a modification-specific antibody, and antibodies against novel UFD1 and PTN6 phosphorylation sites.

A method is provided for producing motif-specific, context-independent antibodies which recognize a plurality of peptides or proteins within a genome that contain the same motif. The method includes the step of immunizing a host with a degenerate peptide library antigen featuring (i) a fixed target motif containing one or more invariant amino acids including at least one modified amino acid, and (ii) a plurality of degenerate amino adds flanking the motif. Motif-specific, context-independent antibodies produced by the disclosed method are also provided. The method encompasses motifs consisting of a single modified amino acid, as well as short motifs comprising multiple invariant amino acids including one or more modified amino acids, such as all or part of kinase consensus substrate motifs, protein-protein binding motifs, or other cell signaling motifs. Methods of using the antibodies, e.g. for genome-wide profiling, are also provided.

Production of motif-specific and context-independent antibodies using peptide libraries as antigens

The invention provides a method for identifying and quantifying polyglycopeptides in a sample. The method can include the steps of immobilizing glycopolypeptides to a solid support; cleaving the immobilized glycopolypeptides, thereby releasing non-glycosylated peptides and retaining immobilized glycopeptides; releasing the glycopeptides from the solid support; and analyzing the released glycopeptides. The method can further include the step of identifying one or more glycopeptides, for example, using mass spectrometry.

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Seattle, WA, United States of America

Hui Zhang