58 results about "Quantitative proteomics" patented technology

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

The invention discloses a method for screening a biomarker related to severe oligoasthenospermia. The method comprises carrying out deep mass spectrometry on multiple sperm protein uncoded amino acids of severe oligoasthenospermia through a NanoHPLC-MS / MS mass spectrometry system and an unlabeled quantitative proteomics method, searching the mass spectrometry data through a nonfinite amino acid protein modification analysis method, carrying out multivariable gaussian mixture distribution clustering analysis to identify the non-coding amino acids in the sperm protein group as much as possible, and comparing the non-coding amino acids of the normal and patient sperm protein groups to obtain protein uncoded amino acid sites related to severe oligoasthenospermia, wherein the protein uncoded amino acid sites are used as molecular markers of severe oligoasthenospermia. The method provides novel diagnostic and therapeutic targets for severe oligoasthenospermia.

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.

Disclosed are methods for producing peptide standards for quantitative proteomics. In one disclosed embodiment, chimeric polypeptides that are a combination of mass tags for multiple proteins are expressed in a host cell that is grown on an isotopically-altered medium. The mass tags in the chimeric polypeptide are separated by specific cleavage sites (such as trypsin cleavage sites), and upon treatment with an appropriate protein cleavage agent (such as trypsin) the constituent peptide standards are released. Methods of mass spectrometric analysis that employ the disclosed chimeric polypeptides (or the peptide standards liberated therefrom) also are disclosed.

The invention relates to a novel solid phase extraction (SPE) device capable of achieving the whole process of quantitative analysis pretreatment of protein. According to the device, an SPE tube is partitioned into two chambers with the same capacity through a partition plate, and after the chambers are filled with chromatographic packing, the whole process of sample treatment in quantitative proteomics can be achieved in situ, wherein the treatment comprises denaturation, reduction, alkylation, enzymolysis, isotope labeling and mixing of protein samples. The device is easy and convenient to manufacture and low in manufacturing cost, and has the advantages that the recovery rate is high, operation is easy, the accuracy of quantitative results is good and the precision is high when the samples are treated.

The invention relates to a method for detecting differentially-expressed protein. For quantitative proteomics, on the basis of marked and unmarked relative quantitative data analysis of primary spectrogram information, whether certain protein differentially expresses protein is judged according to corresponding spectrogram signal intensity ratio of the certain protein in two or more samples, and the method comprises the following steps: matching a peptide spectrum, evaluating credibility, extracting peptide fragment signals, calculating a peptide fragment ratio, calculating a protein ratio, and performing statistical analysis. For about 100 GB data collected through mass spectrum experiment, automated analysis is performed rapidly, for signals of different protein in a mass spectrometer, the protein signals can be extracted accurately as soon as possible, protein differential expression is determined from statistical significance, and accuracy of results is evaluated.

The present invention provides a reagent kit of global analysis for protein expression and method for qualitative and quantitative proteomic analysis using the same, characterized in which isotope labeling reagent is utilized to modify enzymatically cleaved peptides in normal or perturbed cells and subsequently tandem mass spectrometry is used to identify protein sequence, and at the same time, accurately measure the protein expression level based on variation in signal intensity.

The invention provides a method for analyzing data of prokaryotic proteogenomics rapidly and automatically. Users only need to provide mass spectral data and a corresponding database file and set a simple retrieval parameter; retrieval of data of proteogenomics can be completed; simultaneously, a user defined data retrieval result can also be compatible; therefore, the identification coverage rate of the data of proteogenomics is increased; in the method disclosed by the invention, library search engines of different algorithms are integrated in advance; disadvantages of a single retrieval method are made up; a user defined library search result can also be compatible; the method has good compatibility; the peptide fragment identification coverage rate is increased to the most extent; in the method disclosed by the invention, functional annotation of new genes is automatically completed; large-scale identification of protein post-translational modification and analysis of non-labelled quantitative proteomics are realized for the first time; and automatic and rapid deep analysis of the data of proteogenomics is really realized.

The invention relates to a protein chromatographic separation platform and application thereof. The platform comprises a proteome reactor (1) and a liquid phase chromatography-mass spectrometer (2), wherein the proteome reactor (1) comprises a pipette head (3), strong negative-ion exchange resin (4) and a solid-phase extraction membrane (5); the lower end of the pipette head (3) is filled with the solid-phase extraction membrane (5); the strong negative-ion exchange resin (4) is filled at the lower end of the pipette head (3) and is positioned on the solid-phase extraction membrane (5). The protein chromatographic separation platform provided by the invention integrates pre-concentration, reduction, alkylation, enzymolysis, strong negative ion exchange and grading of polypeptides, high pH value reverse phase grading and low pH value liquid-phase chromatography separation, has one-dimensional separation, two-dimensional separation and three-dimensional separation working modes, and can be applied to large-scale authentication and quantitative proteomics of proteins in a small amount of cells, tissues or blood samples.

A labeling reagent having a distinct Raman, or surface enhanced Raman, spectral signature is used for the control and analysis samples. The labeling reagents can be fluorescent dyes with different isotopic substituents, such as the substitution of some hydrogen atoms for deuterium atoms. Such labeling does not have any detectable effect on separation retention. Raman spectroscopy is used for detection purposes. By combining SERS and SERRS, a concentration ratio prediction error of less than 3% can be obtained over four orders of magnitude of total concentration with up to a factor of 3 concentration ratio range. The method is reliable, reproducible and more sensitive than methods based on absolute SERS / SERRS intensity correlations, with no internal standard, or using a different molecule (rather than an IEIS) as a SERS / SERRS internal standard.

The invention relates to an interface for microcolumn liquid chromatogram and mass spectrum, in particular to a capillary monolithic column spray needle. The capillary monolithic column spray needle comprises a capillary pipe, the capillary pipe is filled with monolithic material, a needle head used for electron spray extend at one end of the capillary pipe to form a capillary monolithic column spray needle, then the capillary monolithic column spray needle is connected to the tail end of a capillary separating column through a two-way pipe and the voltage used for electron spray is applied to the two-way pipe. The invention has the main advantages that because the dead volume existing in an electron spray needle in the combined use of the microcolumn liquid chromatography and the mass spectrum and the electron spray needle is eliminated, the capillary monolithic column spray needle eliminates the disturbance and the mixing action of the dead volume to the microcolumn liquid chromatography is eliminated, greatly enhances the separating capacity and the repeatability of the microcolumn liquid chromatography and represents superior performance to the commercial capillary electron spray needle in the quantitative proteomics; and in addition, because the monolithic column material exists in the capillary monolithic column spray needle, the problem that the electron spray needle is easy to be blocked during the separation and the analysis process is solved and the service life of the electron spray needle is greatly prolonged.

The present invention provides a reagent kit of global analysis for protein expression and method for qualitative and quantitative proteomic analysis using the same, characterized in which isotope labeling reagent is utilized to modify enzymatically cleaved peptides in normal or perturbed cells and subsequently tandem mass spectrometry is used to identify protein sequence, and at the same time, accurately measure the protein expression level based on variation in signal intensity.

This invention provides to rare earth element metal chelation label protein for quantitative protein study method and agent case. This invention method relates to protein restore alkali base and pancreatic enzymes slices, peptide section double function agent decoration, rare metal chelation, multi-diemension liquid phase spectrum isolation and multiple degrees series spectrum quantitative and testing. Through one degree spectrum ion signal intensity content and protein validating through series mass spectrum and database. This invention also describes this method agent case.

The invention relates to the technical field of proteomics, in particular to a data analysis method for quantitative methods for b, y fragment ion pairs on second-level mass spectra from peptide fragments of same mass on first-level mass spectra. The method is written by using a Matlab language and runs in a Matlab interface, and qualitative information of peptide fragments and protein is obtained by making ratio through extracting peak intensity information of b, y fragment ion pairs on tandem mass spectra and on the basis of a qualitative result of protein obtained by a SEQUEST search engine. According to the method, an optimization module for 'spectrogram resolution' is also added, so that the influence of a b, y fragment ion pair fragmentation spectrogram on the qualitative correctness of the peptide fragments is reduced. According to the method, a z statistical magnitude is also constructed to calculate the significance of quantitative protein, so that a reference evidence is provided for determining up-regulated and down-regulated changed protein in a practical sample. The invention provides a universal, open and accurate quantitative analysis means for development and application of novel quantitative proteomics methods for the b, y fragment ion pairs on second-level mass spectra from peptide fragments of same mass on first-level mass spectra.

The invention discloses application of an anti-PDCD4 (Programmed Cell Death 4) antibody in preparation of a detection reagent for predicting personalized medicine sensitivity of paclitaxel or a derivative drug of paclitaxel. The variation of protein abundance of whole cells in tumor cells treated by paclitaxel is analyzed by using a quantitative proteomics technology, the results shows that paclitaxel reduces the expression level of PDCD4 and the sensitivity of the tumor cells to paclitaxel is in positive correlation with the expression level of PDCD4 in cells. PDCD4 in the tumor cells is subject to gene silencing or overexpression and the result further proves that the sensitivity of the cells to paclitaxel is in positive correlation with the expression level of PDCD4 in the cells. Meanwhile, researches on survival prognosis of clinical lung cancer patients shows that under the same paclitaxel combined adjuvant chemotherapy, the survival prognosis of patients with low expression level of PDCD4 is poor and the survival time of patients with high expression level of PDCD4 is long. Based on the research results, the invention provides a reference index and a detection and application method for guiding personalized medicine of paclitaxel or the derivative drug (such as docetaxel) of the paclitaxel.

The invention particularly relates to an application of RSPH9 as a diagnosis marker or a treatment target for oligoasthenozoospermia. Sperm proteins of normal and patients are extracted, bovine serumalbumin is used as a standard substance, and multiple groups of sperm proteins of severe application of RSPH9 as a diagnosis marker or a treatment target for oligoasthenozoospermia diseases are subjected to deep mass spectrometry by using high-resolution biomass spectrometry and a non-labeled quantitative proteomics method; the mass spectrum data are searched by using a protein quantitative analysis method, and the protein in the sperm is identified; and finally, normal and patient sperm proteomes are compared, and screening is conducted to obtain that the contents of RSPH9 in healthy and oligoasthenosperm samples are remarkably different. ROC analysis further verifies that RSPH9 has good specificity as a diagnostic marker, and is expected to be used as a diagnostic marker and a treatmenttarget for severe oligoasthenozoospermia.

The invention discloses a method for evaluating the freeze thawing degree of meat based on iTRAQ labelled protein. According to the method, quantification and quantification of protein in the meat subject to freeze thawing treatment are performed by using iTRAQ labeled quantitative proteomics, the protein in which the protein level has obvious difference in the meat subject to the freeze thawing treatment is used as the labeled protein to judge the freeze thawing degree of the meat according to the content of the labeled protein in the meat. The protein in the meat subject to the freeze thawing treatment is verified for the first time by the method disclosed by the invention to provide reference for screening the labelled protein that reflects the quality of the freeze thawing quality of the meat, and the freeze thawing degree of the meat can be judged according to the protein level result, a new quality evaluation method is provided, which is conducive to creating more benefits for meat enterprises, and the application prospect is broad.

The invention discloses a method for monitoring and qualification of 15N metabolic labeled protein in combination with mass spectrum parallel reaction. 15N metabolic labeled internal reference proteincan accurately reflect the structure and the state of endogenous protein to be detected, has the same enzymolysis efficiency with the protein to be detected, solves the problem that internal reference peptide ion strength signals are affected by protease digestion, co-elute matrix, sample composition and instrument status during mass spectrum selection, tracking and quantification to cause nonreproducibility, and meanwhile improves the efficiency of monitoring and qualification of mass spectrum parallel reaction; in addition, the method can produce various quantitative polypeptide used for parallel reaction monitoring, improves the qualification accuracy, reduces the cost for synthesizing polypeptide, can be applied to quantitative proteomic research and detection of protein markers, andhas great help in medical diagnosis, environmental health, food safety inspection and judicial expertise.

The invention generally relates to metabolic labeling of a target organism with a stable isotope. In a first aspect, the present invention relates to a method for metabolic labeling of a target organism with a stable isotope. The present invention also relates to a method of producing a diet for metabolic labeling of a target organism and to a diet composition for metabolic labeling of a target organism. In a further aspect the invention describes the use of the diet composition according to the present invention for producing a metabolically labeled target organism as a reference for a quantitative proteomic approach. The present invention also relates, in a further aspect, to the use of a diet composition for pulse SILAC labeling. The present invention also relates to the use of a target organism labeled by the method according to the first aspect of the present invention as a spike-in standard in quantitative proteomics approaches.

Systems, kits, and methods for detecting and quantifying proteomic activity using DNA-encoded probes are provided, where the proteomic activity may be enzymatic activity or ligand binding affinity. Such systems and methods encode quantitative proteomic activity information into DNA sequence populations and utilize DNA-linked substrates or ligands as activity probes. The systems, kits, and methods that are directed to detecting ligand affinity further include crosslinking steps to ensure the integrity of the DNA-linked ligands during purification and washing. Signal detection involves the chemical manipulation of a probe population downstream of sample exposure and application of purifying, selective pressure for desired products. Selection-induced changes in DNA abundance between the initial pool and the purified pool indicate sample activity.

The invention discloses a capsicum annuum CMS male sterility gene Ca06g18730 based on fertility differential protein. The nucleotide sequence of the capsicum annuum CMS male sterility gene Ca06g18730is shown as SEQ ID NO. Anther specific gene Ca06g18730 related to the capsicum annuum CMS character is identified by utilizing a quantitative proteomics technology, and it is clear that anther of sterile line plants is changed from the meiosis quadruple period, so that pollen abortion is caused; the expression of the maintainer line capsicum annuum Ca06g18730 gene is silenced through a VIGS technology, it is indicated that the CA06g18730 gene plays a key role in the pollen development process, and down-regulation of the CA06g18730 gene is an important factor causing pollen abortion of the CMSsterile line; a VIGS technology is utilized to silence the expression of the capsicum annuum Ca06g18730 gene, so that plant pollen abortion is caused, a capsicum annuum male sterile material is created, and a new material is provided for capsicum annuum breeding.

Systems, kits, and methods for detecting and quantifying proteomic activity using DNA-encoded probes are provided, where the proteomic activity may be enzymatic activity or ligand binding affinity. Such systems and methods encode quantitative proteomic activity information into DNA sequence populations and utilize DNA-linked substrates or ligands as activity probes. The systems, kits, and methods that are directed to detecting ligand affinity further include crosslinking steps to ensure the integrity of the DNA-linked ligands during purification and washing. Signal detection involves the chemical manipulation of a probe population downstream of sample exposure and application of purifying, selective pressure for desired products. Selection-induced changes in DNA abundance between the initial pool and the purified pool indicate sample activity.

The invention relates to mycobacterium tuberculosis Rv0859 protein as a diagnosis marker in tuberculosis diagnosis. The Rv0859 protein is an amino acid sequence shown in SEQ ID No.1 or a variant of the sequence, which is protein having the same function. The invention also relates to preparation of an antibody for resisting Rv0859 as well as detection application of the anti-Rv0859 antibody as anactive component in tuberculosis diagnosis. A quantitative proteomics method finds that secretion level of the Rv0859 protein is significantly improved under an anaerobic culture condition and the Rv0859 can be used as the marker for diagnosis of tuberculosis; recombination expression in vitro is performed on the Rv0859, recombinant protein is used as an antigen to immunize animals, high-concentration pure anti-Rv0859 antibody is obtained, and the antibody can specifically detect Rv0859 protein of mycobacterium tuberculosis; and on the basis that the effective antibody is obtained, an immunohistochemical detection method with Rv0859 as the detection marker is established, which indicates that a new immunohistochemical detection method for tuberculosis can be established by the anti-Rv0859antibody.

The invention discloses an amniotic fluid proteomics detection method of a premature delivery prediction marker and application thereof and relates to the technical field of genetic engineering. The method comprises the following steps of obtaining amniotic fluid differential expression proteins of premature delivery patients (excluding cervical factors) and full-term delivery normal control pregnant women through a liquid chromatography-mass spectrometry method; carrying out GO functional characterization and KEGG pathway analysis on the differentially expressed protein; and verifying the selected candidate protein by using an enzyme-linked immunosorbent assay. The TMT-labeled quantitative proteomics method is used for comparing protein expression differences in amniotic fluid of premature delivery patients (excluding cervical factors) and amniotic fluid of full-term delivery pregnant women. Bioinformatics analysis shows that 44 differential expression proteins and 9 main ways may participate in premature delivery. Subsequent ELISA detection proves that SEPRIN-A1 and IGFBP-4 have significant correlation with premature delivery, and a new thought and approach are provided for prevention and mechanism clarification of premature delivery.

The invention relates to methods and biomarker for evaluating cancer metastasis, pharmaceutical composition for inhibiting cancer metastasis, and method for analyzing secretome. By combining a hollow fiber cartridge (HFC) culture system with quantitative proteomics technology, cancer metastasis-related secrectomes can be found. Furthermore, this is the first time to use PARK7 as a biomarker for judging the process of non-small cell lung cancer.

The invention belongs to the technical field of biomedical engineering, and relates to a new application of an NSrp70 gene, in particular to an application of the NSrp70 gene in preparation of tumor metastasis related pharmaceutical preparations. The nuclear protein quantitative proteomics analysis is carried out on breast cancer cells; the results show that the nuclear speckle protein NSrp70 shows low expression in breast cancer cells with high metastasis potential, the in-vitro and in-vivo experiments prove that the interference of NSrp70 can significantly promote the metastasis ability of the cells, and overexpression of the gene can significantly inhibit the metastasis ability of the cells; the NSrp70 can inhibit cell EMT by inhibiting a TGF beta signal path, and finally breast cancermetastasis is inhibited; the NSrp70 can be used as a new molecular target and a molecular marker in a breast cancer metastasis process to be applied to preparation of breast cancer metastasis relatedmedicaments, including preparation of a detection kit for detecting cancer metastasis, a medicine for inhibiting cancer metastasis and a medicine for inhibiting a cancer metastasis related signal path. The novel application is helpful for preventing and inhibiting breast cancer metastasis and benefiting cancer patients.