178 results about "Protein identification" patented technology

Abstract of Disclosure A genomic web portal is described that receives from a user over the Internet a selection of identifiers of probes for detecting biological molecules. The portal may also receive hybridization intensity values produced from biological probe array experiments. The portal determines alternative splice variants based on factors that may include the hybridization intensity values. The portal correlates alternative splice variants with annotation data and provides for the user a graphical representation of the alternative splice variants and the correlated annotation data. The selection of annotation data to be displayed may be based on a user selection of a genomic, primary-transcript, mRNA, or protein display type. The annotation data may include genomic sequence; presence or relative abundance of alternative splice variants; exon arrangement, content, or sequence; frequency of exon usage in alternative splice variants; RNA, gene, or protein identification, function, structure, or sequence; probe arrangement; and other data.

The invention provides methods, reagents and kits for amino acid, peptide and protein identification, differential quantitation and for the analysis of post translational modification and cross-linking status, comprising: derivatizing a mixture of amino acids peptides or proteins, to form at least one amino acid peptide or protein containing a fixed-charge ion, other than at the C-terminal or N-terminal end thereof; introducing the mixture of amino acids peptides or proteins containing the fixed charge derivatized amino acid peptide or protein to a mass spectrometer; passing the mixture of amino acids peptides or proteins containing the fixed charge derivatized amino acid peptide or protein through a first mass resolving spectrometer to select precursor protein or peptide ions having a first desired mass-to-charge ratio; subjecting the precursor ions of the first mass to charge ratio to dissociation to form a product ion having a second mass-to-charge ratio that is characteristic of a fragmentation occurring at a site adjacent to the fixed charge; and detecting the product ions having the second mass-to-charge ratio. The product ion having the second mass-to-charge ratio may be either a product ion formed by neutral loss of the fixed charge from the precursor ion, or a product ion formed by charged loss of the fixed charge from the precursor ion.

A practical mass spectrometer for proteome analysis is provided. In an ion trap-connected, orthogonal acceleration type time-of-flight mass spectrometer, the mass-to-charge ratio range that may be analyzed by one procedure is increased by providing means for reducing the velocity of ions ejected from an ion trap. The efficiency in protein identification in proteome analysis is thereby improved.

Mass spectrometry is used to identify a protein of interest. The protein is first ionized then fragmented into protein product ion. Masses of the observed product ions are compared to product ion masses calculated in silico for database protein sequences to identify product ion matches within a predetermined mass tolerance. An algorithm that weights the product ion to matches based upon one or more factors such as product ion abundance, favored cleavage sites, product ion type, precursor ion charge state and polarity is used to score the possible matches to database proteins in order to identify the protein of interest. The invention represents a “top down” approach and is particularly well-suited for identification of a protein in a complex mixture.

Arginine-containing cysteine-modifying compounds useful for MALDI-MS analysis of proteins are provided. 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.

A method of combining ES (ElectroSpray Ionization) and MALDI (Matrix Assisted Laser Desorption Ionization) to create enhanced MALDI mass spectrometry to be referred to as ESMALDI (ElectroSpray Matrix Assisted Laser Desorption Ionization). ESMALDI technology offers substantial advantages over conventional technology. essentially by combining the high ionization efficiency and multiple charging of ions in ESI with the smaller sample requirements and operational simplicity of MALDI. Biologists should thus be able to achieve higher sensitivity, better protein identification, enhanced quantification potential and enhanced structural information. An additional degree of freedom for ESMALDI MS is flexibility in the choice of solvents that can be used in the ESI component of the process. Substantial differences in ESI behavior can occur with the same analyte or mixture of analytes in different solvents. Such differences often provide clues to the properties of the analyte and its ions which cannot be readily obtained from conventional MALDI experiments.

The invention discloses a key protein identification method based on subcellular localization specificity. The method includes the first step of establishing subcellular localization protein interaction subnets; the second step of measuring confidence levels of protein key scores of all the subcellular localization interaction subnets of all proteins; the third step of calculating key comprehensive scores of all the proteins; the fourth step of outputting the result, wherein all the proteins in a cell are ranked according to the key comprehensive scores, and the ranking result is output. The key protein identification method based on the subcellular localization specificity is high in accuracy and sensitivity in the identification aspect of key proteins.

The present invention relates to a protein pretreatment and polypeptide high-pH reverse-phase gradation-integrated proteome reactor and the application thereof. The proteome reactor comprises a pipette gun head (1), a strong ion-exchange resin filler (2) and a solid-phase extraction membrane (3). The solid-phase extraction membrane (3) is filled in the lower end of the pipette gun head (1) and is positioned above the solid-phase extraction membrane (3). The proteome reactor provided in the invention integrates the operations of protein pre-enrichment, reduction, alkylation, enzymatic hydrolysis, polypeptide desalination, elution and high-pH reverse-phase gradation, thus being applicable to the large-scale protein identification and the quantitative proteomics for a small number of cells or tissue samples. In addition, the proteome reactor technology can realize the automated liquid handling platform-based automatic operation, such as the Agilent bravo platform-based automatic operation. Therefore, the sample processing throughput and the accuracy of the quantitative analysis are improved.

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

The invention relates to a database searching method and a database searching system for open type protein identification. The database searching method comprises the steps of step 1, inputting protein sequences, simulating and splitting each protein sequence, ranking all generated subsequences according to mass, generating a peptide sequence data list, and establishing an index file according to the peptide sequence data list; step 2, inputting mass spectrums, generating a search set by extracting spectrum peaks from each mass spectrum, searching the index file, and obtaining a sequence set; step 3, generating a candidate peptide fragment according to decoration and combination on each mass spectrum and the sequence set corresponding to each mass spectrum, and marking the candidate peptide fragment; step 4, integrating a marking result, inferring from the peptide fragment to protein, and obtaining an identification result. According to the database searching method disclosed by the invention, the protein identification is carried out in a way that a user is allowed not to assign the types of digestion and decoration or is allowed to assign arbitrary types among the types, and the database searching method is used for solving identification problems of digestion and decoration in the arbitrary types.

The invention provides an index acceleration method in scale protein identification, which comprises the following steps of: setting quality intervals for peptide sequences; setting the size of counting windows, and setting the number of the counting windows and the range of each counting window by combining the quality intervals; performing simulated enzyme digestion on protein database, and calculating the quantity of the peptide sequences in each counting window according to the quality of the peptide sequences obtained through the simulated enzyme digestion; obtaining the quantity of the peptide sequences which can be processed once in the memory of a computer according to the capacity of the memory of the computer, and obtaining a quality range section of the peptide sequences which can be processed once in the memory of the computer by combining the quantity of the peptide sequences in each counting window; performing the simulated enzyme digestion on the protein database, saving the obtained peptide sequences in one quality range section in the memory of the computer, and finishing the operations of sequencing, redundancy removal, and dictionary and inverted list establishment on the saved peptide sequences in the memory of the computer; and establishing a dictionary and an inverted list for each quality range section.

Methods of-identifying a basal or luminal phenotype of a cell, comprising detecting expression of one or more of a set of predictive biomarker genes or proteins that identify the cell as having a basal or luminal cancer subtype and compositions for treating identified basal or luminal cancers.

The invention discloses a method for measuring ancient cowhair micro-trace based on proteomics. A soil sample of the ancient cowhair micro-trace, a soil sample of a surface soil layer and a soil sample of a raw soil layer are extracted and separated, protein is effectively separated by a two-dimensional electrophoretic technique, the electrophoretic results of the three samples are compared, the influence that the soil contains protein and the interference of external factors are excluded, stripes in the electrophoretic results are cut off and subjected to in-gel digestion, mass spectrometric analysis is conducted, and protein identification can be realized by comparing the mass spectrometric analysis result with the amino acid sequence in a protein database. The ancient cowhair micro-trace is measured by a proteomic method, the problem that the common analysis test is helpless during analysis of micro-trace residues is solved, the protein varieties of the samples are obtained accurately through proteomic measurement, and whether the micro-trace sample is the cowhair micro-trace is judged, so that on one hand, the method is high in sensitivity and is simple and convenient to operate, and on the other hand, the use amount of the samples is small.

The invention relates to a protein identification method based on a two-end equal-weight label and database search and belongs to the technical field of biological information. According to the identification method, a protein enzymolysis product obtained by performing isotoplabelling at the two ends of polypeptide is subjected to separation and detection through liquid chromatogram-mass spectrum combination; when identification is conducted by a database search method, identification of polypeptide is realized by establishing a peptide fragment theory spectrogram containing all the fragment ions of the peptide section formed by two labels and matching with the experimental mass spectrogram, so that the protein is obtained through identification, the identification efficiency of polypeptide and the protein is improved, and the method can be used for efficiently identifying the protein sample of the database.

The present invention describes a method of selective peptide isolation for the identification and quantitative analysis of proteins in complex mixture. The method comprises the selective isolation from every protein of those peptides that neither contain arginine nor histidine (NHNR peptides), and the determination of the relative concentrations of one or several proteins in different samples from the ratio between the areas of the estimated theoretical spectra for the NHNR peptides labeled with different isotopes in each sample. The determination of the relative concentration of proteins is valid for any type of isotopic label of the NHNR peptides. The method avoids the separation and purification of the proteins present in a complex mixture, and the analysis of all peptides generated from the enzymatic digest of the samples. The method is applicable to the identification of proteins with vacunal, therapeutic and diagnostic aims.

The present invention provides methods for purifying RNA molecules interacting with an RNA binding protein (RBP), and the use of such methods to analyze a gene expression profile of a cell. The invention also provides sequences of RNA molecules that mediate binding to an RBP, proteins encoded by the sequences, a method of identifying the sequences, and the use of the sequences in a screen to identify bioactive molecules. The invention also provides RNA motifs found among the sequences and compounds that bind the RNA motifs. In addition, the invention provides methods of treating diseases associated with a function of an RNA binding protein.

The present teachings describe methods for matching a query peptide to a database of known peptides based on a mass analysis approach. The methods described herein facilitate rapid, sensitive, and selective identification of an unknown query peptide and provide the ability to develop applications which perform substantially automated high throughput protein identification. The methods described herein also allow for mass spectrometry data for a query peptide to be categorized and weighted according to its quality. Furthermore, the methods described herein provide robust identification of modified query proteins by either anticipating modifications or adjusting for modified peptide masses.

The invention relates to an algorithm for identifying a key protein based on a genetic algorithm in a PPI network. The algorithm comprises the steps of generating an initial population in a protein interaction network; calculating the fitness of individuals; performing selection operation by a roulette wheel method; performing crossing operation and mutation operation among the randomly selected individuals; and performing local optimization on multiple individual solutions. According to the algorithm, the defects of existing methods are overcome; indexes are optimized and bio-information is fused, so that the reliability is higher and lots of unnecessary calculations are reduced; and the predicted key protein can be locally optimized, so that the efficiency of key protein identification is improved, and the application range and practicality of the technology in the field of the bio-information are expanded and improved.

The invention relates to a large-scale distributed parallel acceleration method and system for protein identification. The method comprises the following steps of: by a parallel processing method, theoretically digesting a protein sequence to obtain peptide sequences, and sorting and redundantly processing the peptide sequences so as to create a peptide index file block; sorting mass spectra spectrums, and evenly dividing the sorted mass spectra spectrums into a plurality of spectrum data blocks; and evenly distributing the spectrum data blocks to a plurality of host processes, and each host process sorting the distributed spectrum data blocks and sequentially assigning to idle slave processes for peptide spectrum matching identification; and summarizing identification results by the parallel processing method, inferring the corresponding protein sequences by the peptide sequences obtained by identification, and generating output files. When a processor has hundreds or even thousands of cores, the satisfactory acceleration efficiency when the protein identification is carried out can be obtained.