48 results about "Protein Sequence Determination" patented technology

The invention provides cubilose peptide and a key preparation method of cubilose peptide maternity cubilose, and the preparation method of the cubilose peptide comprises the following steps: soaking dry cubilose in pure water at 0-4 DEG C according to a material-liquid ratio of 1: 10 for 2 hours, scattering, and spin-drying to obtain soaked cubilose; mixing the soaked cubilose with pure water according to a mass ratio of 1: (15-20), sealing, stewing at 121-123 DEG C for 12-15 minutes, cooling to room temperature, and repeatedly stewing once to obtain fresh stewed cubilose; carrying out an in-vitro digestion experiment on the freshly stewed cubilose, and simulating the digestion process of the freshly stewed cubilose in gastrointestinal tracts to obtain digested cubilose; and centrifuging the digested cubilose to obtain a supernatant, treating the supernatant, carrying out protein sequencing, and carrying out on-line database comparison to screen out peptide fragments with high matching degree and response value greater than 109, thereby obtaining the cubilose peptide. The cubilose peptide can significantly improve the proliferation rate of nerve cells, and provides a cell basis for the development of a nervous system.

Provided herein are methods and systems for sequencing proteins. One or more methods disclosed herein may use linkers having an amino acid-reactive group and an additional reactive moiety that may be used to couple a polymerizable molecule. The linker may couple to a polymerizable molecule and an amino acid of a peptide and a capture moiety via the polymerizable molecule, followed by cleavage of the amino acid from the peptide. Further processing and analysis may be conducted using, for example, nanopores or nanogaps.

Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides amino acid recognition molecules, such as amino acid binding proteins and fusion polypeptides thereof. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.

Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same. In some aspects, the application provides methods of obtaining data during a degradation process of a polypeptide, and outputting a sequence representative of the polypeptide. In some aspects, the application provides amino acid recognition molecules comprising a shielding element that enhances photostability in polypeptide sequencing reactions.

The present disclosure provides reagents and methods useful for single-molecule sequencing of proteins through use of a unique sequencing reagent comprising a xanthate group. The reagents and methods described herein provide for high-throughput single-molecule peptide and protein sequencing in mild conditions allowing for high resolution investigation of the complex biological systems.

Provided herein are methods and systems for sequencing proteins. One or more methods disclosed herein may use linkers having an amino acid-reactive group and an additional reactive moiety that may be used to couple a polymerizable molecule. The linker may couple to a polymerizable molecule and an amino acid of a peptide and a capture moiety via the polymerizable molecule, followed by cleavage of the amino acid from the peptide. Further processing and analysis may be conducted using, for example, nanopores or nanogaps.

The present invention relates to the field of biochemistry, more particularly to proteomics, more particularly to protein sequencing, even more particularly to single molecule peptide sequencing. The invention discloses means and methods for single molecule protein sequencing and / or amino acid identification using cleavage inducing agent. Said cleavage inducing agents which are not specific for one particular amino acid, cleave polypeptides step by step from the N-terminus onwards and provide information on the identity of the cleaved amino acids based on the kinetics of said reaction.

Disclosed herein are methods for preparing a biological sample for single-cell analysis which will simultaneously provide single-cell RNA, single-cell extracellular protein, single-cell cytoplasmic protein, and single-cell transcription factor readouts while preserving cellular heterogeneity. Some methods disclosed herein allow for the detection of proteins including the detection of the level of proteins and / or the detection of post translational modifications of proteins.

This application provides a method, related methods, and apparatus for processing protein sequencing data, relating to the field of protein sequencing technology. The method for processing protein sequencing data involves acquiring protein sequencing data of a target protein from a target slice, determining the frequency of each protein signal intensity value in the sequencing data, and calculating the probability of each protein signal intensity value based on the frequency; calculating a protein signal intensity threshold to classify protein signal intensity based on the protein signal intensity value and probability; and identifying sequencing sites with protein signal intensity values ​​greater than the protein signal intensity threshold as foreground sites corresponding to the target protein. Since the protein signal intensity threshold is calculated based on the protein signal intensity value and probability, using the protein signal intensity value and probability as defining factors for the protein signal intensity threshold helps to reasonably and accurately determine the threshold used to distinguish positive and negative signals, thereby facilitating more precise identification of foreground sites.

This invention belongs to the field of protein sequencing, specifically disclosing a novel solid-state sub-nanopore fabrication method and its application in protein sequencing. The technical solution involves: reliably and easily fabricating pores with a diameter less than 1 nm on a 5 nm thick pure silicon film; reconstructing the spatial structure of the pores in three dimensions at the atomic scale through transmission electron microscopy imaging and multilayer image simulation comparison; and then incorporating key geometric parameters into finite element multiphysics modeling to simulate the electric field distribution within the pores and calculate the conductivity of the sub-nanopores, thereby evaluating the application potential and performance of this fabrication method in protein single-molecule sequencing. The sensing region depth of this novel nanopore can be less than 1 nm, giving it an advantage over other similar nanopores in developing protein de novo sequencing technology with single-point residue specificity (kmer=1), providing a new approach for the single-point residue specificity detection of protein variants.

The application provides a key preparation method of bird's nest peptide and bird's nest peptide for pregnant women, and the preparation method of the bird's nest peptide comprises the following steps: soaking dry bird's nest in pure water at 0-4 DEG C for 2 h at a material-to-liquid ratio of 1:10, beating and then drying to obtain soaked bird's nest; mixing the soaked bird's nest with pure water at a mass ratio of 1:15-20, sealing and then stewing at 121-123 DEG C for 12-15 min, repeating the stewing once after cooling to room temperature to obtain fresh stewed bird's nest; carrying out in-vitro digestion experiment on the fresh stewed bird's nest to simulate the digestion process of the fresh stewed bird's nest in the gastrointestinal tract, and obtaining digested bird's nest; centrifuging the digested bird's nest to obtain supernatant, treating the supernatant, and then carrying out protein sequencing; comparing the protein sequencing with an online database, screening out a peptide segment with high matching degree and a response value greater than 10 9 The bird's nest peptide can significantly improve the proliferation rate of nerve cells, and provides a cell basis for the development of the nervous system.

The invention provides a protein sequencing data processing method, a related method and a related device, and relates to the technical field of protein sequencing. The protein sequencing data processing method comprises the following steps: determining the occurrence frequency of each protein signal intensity value in the protein sequencing data by acquiring the protein sequencing data of a target protein in a target slice, and calculating the occurrence probability of each protein signal intensity value according to the frequency; calculating a protein signal intensity threshold value for carrying out intensity division on the protein signal intensity based on the protein signal intensity value and the probability; and determining the sequencing site with the protein signal intensity value greater than the protein signal intensity threshold as the foreground site corresponding to the target protein. The protein signal intensity threshold value is calculated based on the protein signal intensity value and the probability, and the protein signal intensity value and the probability are used as defining factors of the protein signal intensity threshold value, so that the threshold value for distinguishing the positive signal from the negative signal can be reasonably and accurately determined, and the foreground site can be more accurately determined.

The invention belongs to the technical field of culture media, and particularly relates to a method for evaluating a culture medium raw material soy peptone, which comprises the steps of antibacterial substance detection, microbial growth promotion effect evaluation and soy peptone quality judgment according to a comprehensive evaluation standard. According to the method, the antibacterial substances in the soy peptone are accurately measured through a protein sequencing method, and the quality of the soy peptone can be comprehensively analyzed from multiple dimensions by combining growth data of various indication microorganisms, so that the limitation of a single evaluation index is avoided, the accuracy is greatly improved, the evaluation result is more accurate and reliable, and the method is suitable for large-scale popularization and application. The experiment and production efficiency is improved, the production cost is reduced, and the resource waste is reduced.

The present invention relates to the technical field of protein detection, and discloses a protein detection method based on an arrayed nanopore structure, comprising the following steps: Step 1, processing array grooves on a chip thin film; Step 2, connecting a temperature control element to the bottom of the chip thin film; Step 3, fixing a protein at the bottom of the array grooves; Step 4, covering a phospholipid layer on the surface of the chip thin film; Step 5, electrically driving the embedding of functional proteins. By adopting the above-mentioned protein detection method based on an arrayed nanopore structure, the relative distance between two functional proteins in the nanopore structure can be adjusted by controlling the thickness of the chip film and the processing depth of the grooves, effectively solving the problem of short read lengths caused by the nano-space limitation of the peptide chain. At the same time, the arrayed combined protein sensor can also achieve high-throughput detection of peptide chains, realizing stable, long-read-length, and highly accurate protein sequencing.

The present application discloses a protein marker for early pregnancy detection of mammals, and particularly relates to a hidden marker protein serum amyloid A of early pregnancy test paper. Protein sequencing used in the present application adopts liquid chromatography-mass spectrometry (LC-MS) technology, sample correlation is compared through Venn, sample correlation, PCA and PLS-DA analysis; protein function annotation is carried out through GO, KEGG, COG and Pfam, and subcellular localization prediction is carried out; difference protein, protein set and difference metabolite are calculated and counted; correlation analysis of proteome and transcriptome is carried out, difference protein of sheep serum in early pregnancy is obtained, and a key marker protein of early pregnancy of sheep is screened, which provides a basis for unknown early pregnancy detection of sheep.

Compositions and methods for analysis of protein expression at the single cell level are described. The single cell proteomic technology described herein implements peptide barcode molecules to uniquely label all of the proteins and / or polypeptides present in a single cell, whereby all of the proteins / polypeptides (proteome) present in a single intact cell are uniquely labeled with a peptide barcode molecule in a partition. Polypeptides from a single cell can be uniquely barcoded and via protein sequencing, such as nanopore sequencing. Proteomic analysis of the protein sequencing data elucidates the entire proteome that was expressed in the single cell.

The application provides a polypeptide and protein sequencing method, a kit and application. The polypeptide sequencing method comprises the following steps: S1, attaching a target polypeptide to a nanopore; S2, introducing a recognition molecule specifically recognizing a terminal amino acid of the target polypeptide into a nanopore sequencing system; under the action of an electric field, the detection of the terminal amino acid of the target polypeptide is realized by utilizing the electric signal change generated in the binding and dissociation process of the recognition molecule and the target polypeptide. By utilizing the unique electric signal change generated in the binding and dissociation process of the recognition molecule and the terminal amino acid of the target polypeptide, the detection of a single amino acid is realized.

The invention relates to an anthrax protein nanopore system and application thereof in protein sequencing, and belongs to the technical field of nanopore detection. The invention aims to solve the problems of low flux, insufficient accuracy and limited nanopore resolution in the existing protein sequencing technology. According to the invention, an anthrax protein PA63 heptamer nanopore electrochemical detection device is constructed, an asymmetric pH buffer system is adopted, Trypsin, Calpain-1, Pancreative Elatase, CarboxyceptidaseA enzyme and the like are added step by step for polypeptide enzyme digestion, voltage is applied to drive amino acid to pass through nanopores, current signals are collected, amplitude, retardation time and frequency characteristics are analyzed, and polypeptide amino acid sequence detection is realized. The nanopore is small in opening current (fA level) and high in resolution ratio, detection accuracy and sensitivity are enhanced by combining multi-enzyme step-by-step cutting and carving, and a direct and efficient sequencing means is provided for protein function research.

Provided herein are methods and systems for sequencing proteins. One or more methods disclosed herein may use linkers comprising an amino acid-reactive group and an additional reactive moiety that may be used to couple a polymerizable molecule. The linker may couple to a polymerizable molecule and an amino acid of a peptide and a capture moiety via the polymerizable molecule, followed by cleavage of the amino acid from the peptide. Further processing and analysis may be conducted using, for example, nanopores or nanogaps.

The present disclosure provides reagents and methods useful for single-molecule sequencing of proteins through use of a unique sequencing reagent. The reagents and methods described herein provide for high-throughput single-molecule peptide and protein sequencing in mild conditions allowing for high resolution investigation of the complex biological systems.

The application provides a single-molecule protein sequencing device based on a quantum tunneling electrode, a method and application thereof. First, a tunneling electrode pair with a gap of less than 5 nanometers is prepared, and then an exopeptidase is bridged between the electrodes in a directional manner through asymmetric modification. When the exopeptidase cuts amino acids from the end of a substrate peptide chain, the conformational change of the exopeptidase modulates the tunneling current. The current signal is collected in real time, and the amino acid sequence can be analyzed by using a machine learning algorithm to analyze characteristic fingerprints. Based on this, in the future, the method can be developed into a label-free and real-time single-molecule protein sequencing technology, which can be used for low-abundance proteome analysis, post-translational modification identification and single-cell protein research.

The application discloses a bacillus amyloliquefaciens genome-scale metabolic network model, a construction method and application, and belongs to the field of system biology. The method comprises the following steps: firstly, a rough model of bacillus amyloliquefaciens is automatically constructed according to protein sequencing results of bacillus amyloliquefaciens in a Uniport database; secondly, the rough model is manually refined and the synthesis reaction of acetoin is added according to a literature database, a metabolic pathway diagram and a biochemical database, so as to construct a genome-scale metabolic network model; thirdly, the genome-scale metabolic network model is converted into a computer-readable mathematical model; and finally, the mathematical model is analyzed by using a flux balance analysis method, and compared with experimental values in the literature. The method has the advantages of short construction time, simple operation and high accuracy, can systematically predict the nutritional conditions for the growth of bacillus amyloliquefaciens, and provides a feasible basis for improving the yield of acetoin and industrial production.

Provided are a protein sequencing library construction method and a protein sequencing method. The protein sequencing library construction method comprises: using an endonuclease to carry out enzymatic cleavage on a target protein to obtain two or more polypeptide fragments each containing a free amino group at the N-terminus and the same functional group at the C-terminus, the functional group comprising an amino, ε-carboxyl or phenolic hydroxyl group; using the functional group at the C-terminus and the free amino group at the N-terminus to conjugate each polypeptide fragment to a nucleic acid to obtain a protein sequencing library, wherein the nucleic acid is conjugated to the functional group at the C-terminus and the free amino group at the N-terminus of the polypeptide fragment, respectively. The present invention can solve the problem in the prior art of the difficulty in sequencing of native proteins (i.e., proteins with unknown sequences), and is applicable to the field of protein sequencing.

The present invention provides methods for identifying and sequencing proteins, polypeptides, and amino acids, as well as compositions useful for them. [Solution] The present invention provides amino acid recognition molecules, such as amino acid-binding proteins and their fusion polypeptides, which differentially associate with different types of amino acids to generate detectable characteristic signatures that serve as indicators of the amino acid sequence of polypeptides. The present invention also provides amino acid recognition molecules that include a shielding element to enhance photostability during polypeptide sequencing reactions.

The present invention relates to the technical field of protein detection, and discloses a protein sequencing method based on a nano-motion platform and a nanopore, comprising the following steps: Step 1, fabricating a nano-through hole; Step 2, building a detection platform; Step 3, electrically driving a functional protein to be embedded into a solid-state nanopore, and performing protein detection by using a protein sequencing system. By adopting the above-mentioned protein sequencing method based on a nano-motion platform and a nanopore, the present invention utilizes a sub-nanometer single-molecule manipulation system to adjust and maintain the distance between the driving protein in the holding device and the reading protein in the chip film, overcoming the problem of difficult read length in current protein molecule detection due to the limitation of the nano space.

The present invention provides a polypeptide and protein sequencing method, a kit, and a use. The polypeptide sequencing method comprises: S1, attaching a target polypeptide to a nanopore; and S2, introducing a recognition molecule, which specifically recognizes a terminal amino acid of the target polypeptide, into a nanopore sequencing system, and under the action of an electric field, using an electric signal change generated during binding / disassociation of the recognition molecule and the target polypeptide to detect the terminal amino acid of the target polypeptide. The detection of a single amino acid is achieved by using a unique electric signal change generated during binding / dissociation of the recognition molecule and the recognized terminal amino acid of the target polypeptide.

The present disclosure relates to methods and kits for analyzing a macromolecule analyte in a cyclic manner that incorporate basic steps of the ProteoCode™ protein sequencing assay and in addition incorporate approaches that allow to control template independent nucleotide addition by the DNA polymerase, and thus ensure successful multi-cycling encoding. Three different approaches are proposed herein to prevent heterogeneity in the spacer length of the extended recording tag created during the primer extension reaction. The disclosed methods allow for highly-parallelized, accurate and sensitive macromolecule characterization.

Described herein are techniques for detecting amino acid variants in peptides using data from a sequencing device. Sequencing data is generated from traces of light pulses output by the sequencing device from detecting light emissions by fluorescently tagged N-terminal amino acid (NAA) recognizers during sequencing of at least one peptide. The sequencing data comprising light pulse durations and inter-pulse durations between successive light pulses. The techniques generate read(s) each comprising a sequence of recognition segments indicating time periods in which fluorescently tagged NAA recognizers were binding to particular NAAs of the peptide, assign fluorescently tagged NAA recognizers to recognition segments, align read(s) to reference peptide sequences to obtain peptide alignments, and detect amino acid variants using the peptide alignments.

The present invention relates to a device (2) for sequencing a protein (4) or part thereof, comprising a substrate (6) comprising a first pore (16), the pore providing or adjacent a plasmonic hotspot (22) such that a protein (4) passing through the hotspot (22) can be sequenced using Raman spectroscopy in use. A second pore (18) fluidly connected to and spaced from the first pore (16) and configured to receive the protein (4). The device (2) comprises a means (34A,B) to bias said protein (4) toward the first pore (16) and / or second pore (18), such that the protein (4) passing through the hotspot (22) is at least partially uncoiled, unfolded or otherwise linearised.