54 results about "Proteome profiling" patented technology

Methods and compositions are described for single cell resolution, quantitative proteomic analysis using high throughput sequencing.

The invention provides methods for identifying polypeptides. The method can include the steps of simultaneously determining the mass of a subset of parent polypeptides from a population of polypeptides and the mass of fragments of the subset of parent polypeptides; comparing the determined masses to an annotated polypeptide index; and identifying one or more polypeptides of the annotated polypeptide index having the determined masses. The method can further include the steps of determining one or more additional characteristics associated with one or more of the parent polypeptides; comparing the determined characteristics to the annotated polypeptide index; and optionally repeating the steps one or more times, wherein a set of characteristics is determined that identifies a parent polypeptide as a single polypeptide in the annotated polypeptide index. The method can additionally include the step of quantitating the amount of the identified polypeptide in a sample containing the polypeptide.

Methods and apparatus for qualitative and quantitative proteome analysis are provided. The methods and apparatus 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 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.

The present invention provides novel anther-specific genes, their promoters, and uses of the same. Rice seedlings were treated with gibberellin, and then genes and proteins with up-regulated expression were screened using DNA microarray analysis and proteome analysis. As a result, eight types of β-tubulins were identified. Among them, OsTUB8 was expressed specifically in the anther. Thus OsTUB8 was suggested to be involved in male sterility in rice, and it was thought that regulating OsTUB8 expression in plants could alter plant fertility. In addition, OsTUB8 promoters were thought to comprise anther-specific activity. Thus, the present invention can be said to be highly valuable when used as a tool for anther-specific gene expression.

The present invention relates to phosphate-binding compounds that find use in binding, detecting and isolating phosphorylated target molecules including the subsequent identification of target molecules that interact with phosphorylated target molecules or molecules capable of being phosphorylated. A binding solution is provide that comprises a phosphate-binding compound, an acid and a metal ion wherein the metal ion simultaneously interacts with an exposed phosphate group on a target molecule and the metal chelating moiety of the phosphate-binding compound forming a bridge between the phosphate-binding compound and a phosphorylated target molecule resulting in a ternary complex. The binding solution of the present invention finds use in binding and detecting immobilized and solubilized phosphorylated target molecules, isolation of phosphorylated target molecules from a complex mixture and aiding in proteomic analysis wherein kinase and phosphatase substrates and enzymes can be identified.

Provided are protein microarrays, their manufacture, use, and application. Protein microarrays in accordance with the present invention are useful in a variety preoteomic analyses. Various protein arrays in accordance with the present invention may immobilize large arrays of proteins that may be useful for studying protein-protein interactions to improve understanding of disease processes, facilitating drug discovery, or for identifying potential antigens for vaccine development. The protein array elements of the invention are native or modified proteins (e.g., antibodies or fusion proteins). The protein array elements may be attached directly to a organic functionalized mirrored substrate by a binding reaction between functional groups on the substrate (e.g., amine) and protein (e.g., activated carboxylic acid). Techniques for chemical blocking of the arrays are also provided. The invention contemplates spotting of array elements onto solid planar substrates, labeling of complex protein mixtures, and the analysis of protein binding to the array. The invention also enables the enrichment or purification, and subsequent sequencing or structural analysis of proteins that are identified as differential by the array screen. Kits including protein-binding microarrays for proteomic analysis in accordance with the present invention are also provided.

The present invention relates to phosphate-binding compounds that find use in binding, detecting and isolating phosphorylated target molecules including the subsequent identification of target molecules that interact with phosphorylated target molecules or molecules capable of being phosphorylated. A binding solution is provide that comprises a phosphate-binding compound, an acid and a metal ion wherein the metal ion simultaneously interacts with an exposed phosphate group on a target molecule and the metal chelating moiety of the phosphate-binding compound forming a bridge between the phosphate-binding compound and a phosphorylated target molecule resulting in a ternary complex. The binding solution of the present invention finds use in binding and detecting immobilized and solubilized phosphorylated target molecules, isolation of phosphorylated target molecules from a complex mixture and aiding in proteomic analysis wherein kinase and phosphatase substrates and enzymes can be identified.

The invention aims to provide a method for analyzing proteome in a biological sample. The method can detect unique proteome generated by cancer cells through blood or body fluid in an early stage of tumors; and the method can diagnose cancers more sensitively and more early so as to make early diagnosis and treatment of the cancers possible.

The invention provides a microfluidic system and method to rapidly analyze large numbers of compounds or complex mixtures of compounds, particularly, low abundance cellular proteins involved in cell signaling pathways. In one aspect, an integrated microfluidic system comprises an upstream separation module (preferably, a multi-dimensional separation device), a microfluidic device for on-device protein digestion of substantially separated proteins received from the upstream separation module, a downstream separation module for separating digestion products of said proteins, a peptide analysis module and a processor for determining the amino acid sequence of said proteins. Preferably, the system comprises an interfacing microfluidic device between the downstream separation module and the peptide analysis module.

Improved methods of performing proteomic analysis are described wherein single cell samples are placed into nanowells disposed on chips that also contain a booster sample of known peptides. Once the samples are placed, these singles cells are lysed and peptides are extracted. These peptides are then labeled using TMT labels and combined with labeled boosting peptides to form a mixed sample. The mixed sample is then separated using an LC separation system and the separated sample is then passed through a mass spectrometer to acquire data of the peptide characterization data from the separated sample. Various modifications and alterations to the MS acquisition process that enhance the effectiveness of the process are also described.

Proteins specific for prostate epithelial cells, normal or neoplastic, are identified and used for diagnosis, development of antibodies, and for evaluating drugs that react with the neoplastic specific proteins. Affinity based probes are used that react specifically with the active site to provide a measure of the enzyme activity of the cells. Prostate epithelial neoplastic cells can be used in screening candidate drugs for their effect in changing the proteome profile as to the serine-threonine hydrolase enzymes, using the affinity based probes for determining the profile.

Provided herein are methods and systems for proteome analysis that are at least partially automated and / or performed robotically. In some aspects, the methods and systems described herein can rapidly and efficiently provide protein identification of each of the proteins from a proteome, or a complement of proteins, obtained from extremely small amounts of biological samples. The identified proteins can be imaged quantitatively over a spatial region. Automation and robotics facilitates the throughput of the methods and systems, which enables protein imaging and / or rapid proteome analysis.

The present invention concerns a method for identifying and using a biomarker, or creating a proteome profile, indicative of a reduced response to a drug in a patient involving a thermal shift assay on a sample. The method comprises the steps of a) heating a sample from a patient b) separating soluble from insoluble protein, c) analysing either or both the soluble and insoluble protein fractions of step b) to determine the melting temperature.