Provided herein are methodologies where a glycosylated protein or peptide is subjected to peptide bond cleavage to produce a glycan amino acid complex wherein the N-linked or O-linked glycan is attached. A derivatization reagent is then attached to the N terminus of the amino acid to provide a labeled glycan amino acid complex. The labeled glycan amino acid complex is then separated from the matrix via one or more methods including HILIC SPE, and injected directly onto an LC or LC/MS system for analysis, detection and characterization of the glycosylated protein or the peptide.

Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

A chemical analysis apparatus that quantitatively determines an object of detection rapidly with high sensitivity, and a pretreatment apparatus and a chemical analysis method used for the chemical analysis apparatus, are provided. The chemical analysis apparatus includes a pretreatment unit that accommodates a molecularly imprinted polymer capable of capturing a polar group-containing molecule included in a specimen. A quantification unit quantitatively determines a component included in the specimen that has been passed through the pretreatment unit.

The present invention relates to sample preparation container for purification and/or enrichment of bio-organic compounds from cellular material, viruses and/or sub-components of said cellular material and/or viruses, the container comprising a reaction chamber and a chromatography medium; wherein said reaction chamber is for holding said cellular material, viruses and/or sub-components of said cellular material and/or viruses and is configured such that at least one of the following reactions can be performed therein: lysis, e.g. by sonication and/or boiling; chromatographic purification; reduction; alkylation; and enzymatic reactions such as proteolysis; wherein said chromatography medium is configured to purify and/or enrich said bio-organic compounds; wherein (a) said chromatography medium is located at a wall of said reaction chamber, and said wall is closed or sealed and configured to be opened for obtaining purified and/or enriched bio-organic compounds; or (b) said sample preparation container further comprises a receiving chamber for receiving said bio-organic compounds, said receiving chamber being adjacent to said chromatography medium such that said chromatography medium separates said reaction chamber from said receiving chamber, and the outer face of said receiving chamber is closed and configured to be opened for obtaining purified and/or enriched bio-organic compounds.

The invention discloses the use of an artificial protein for isolating a nucleosome, the nucleosome comprising a multiple-modified histone protein octamer, wherein the artificial protein comprises a first histone modification binding domain of 50 to 200 amino acids binding to a first histone modification, a second histone modification binding domain of 50 to 200 amino acids binding to a second histone modification, a linker of 5 to 50 amino acids connecting the first and the second histone modification binding domain, and an affinity tag. Further disclosed are a nucleic acid encoding the artificial protein, a host cell comprising the nucleic acid and a kit for isolating a nucleosome, the nucleosome comprising a multiple-modified histone protein octamer. Further disclosed is an in-vitro method for isolating a nucleosome having a first and a second histone modification.

The invention relates to a method for selecting proteins stable in non-standard physicochemical conditions (temperature, pressure, pH, osmolarity, salinity, solvent, etc.) comprising the expression, in an extremophilic microorganism, of variants of the protein of interest in the form of a fusion protein with a reporter protein which is stable in extreme conditions and acts as a selection marker.

There is provided a method of manufacturing a protein array or peptide array suitable for an efficient screening of a functional protein or functional peptide. The method of manufacturing a protein array or peptide array includes the steps of: (a) preparing a nucleic acid immobilized on a solid support and a cell-free synthesis system in a reactor, in which a reactor array includes the reactor having a specific aperture shape and a protein capture molecule or a peptide capture molecule provided on at least a portion of wall surface and bottom surface in the reactor; and (c) synthesizing a protein or peptide from the nucleic acid using the cell-free synthesis system and immobilizing the protein or peptide in the reactor.

Methods and chemicals for the capture and analysis of a selected group of protein modifications. Post-translational modifications alter the functional groups in proteins. The resulting modified proteome is useful for biomarker discovery, clinical diagnostics, and protein dynamics. Present immunoassays to quantify modified proteins are limited by their dependence on antibodies, which are often not specific for post-translational modifications. This invention utilizes a reagent and platform with a binding moiety that is capable of selectively binding to the modified protein.

Protein ubiquitylation, an essential post-translational modification, regulates almost every cellular process including protein degradation, protein trafficking, signal transduction, and DNA damage response in eukaryotic cells. The diverse functions of ubiquitylation are thought to be mediated by distinct chain topologies resulting from eight different ubiquitin linkages, chain lengths, and complexities. Currently, ubiquitin linkages are generally thought to be a critical determinant of ubiquitin signaling. However, ubiquitin chain lengths, another key element of ubiquitin signaling, have not been well documented especially in vivo situation during past three decades from the discovery of ubiquitin. The reason of this was simply because no method has been available for determination of ubiquitin chain length in endogenous ubiquitylated substrates. In the present invention, a practical technique for determining the actual length of substrate-attached polyubiquitin chains from biological samples is established. Using the method, the mean length of substrate-attached polyubiquitin chains was determined and the robustness of ubiquitin chain length regulation in cells is investigated. The following is a summary of findings in this invention: 1. A method for determining ubiquitin chain length was developed and this method was named ubiquitin protection from trypsinization (Ub-ProT). 2. Using Ub-ProT, it was determined that the mean length of substrate-attached ubiquitin chains is in the dimer to decamer range. 3. By quantitative proteomics, it was found that the mean lengths of five major types of ubiquitin chains can be divided into two groups. 4. Proteasome-inhibition did not alter the mean length of substrate-attached polyubiquitin chains, indicating that cells have a robust system for regulating ubiquitin chain length.

Protein ubiquitylation, an essential post-translational modification, regulates almost every cellular process including protein degradation, protein trafficking, signal transduction, and DNA damage response in eukaryotic cells. The diverse functions of ubiquitylation are thought to be mediated by distinct chain topologies resulting from eight different ubiquitin linkages, chain lengths, and complexities. Currently, ubiquitin linkages are generally thought to be a critical determinant of ubiquitin signaling. However, ubiquitin chain lengths, another key element of ubiquitin signaling, have not been well documented especially in vivo situation during past three decades from the discovery of ubiquitin. The reason of this was simply because no method has been available for determination of ubiquitin chain length in endogenous ubiquitylated substrates. In the present invention, a practical technique for determining the actual length of substrate-attached polyubiquitin chains from biological samples is established. Using the method, the mean length of substrate-attached polyubiquitin chains was determined and the robustness of ubiquitin chain length regulation in cells is investigated. The following is a summary of findings in this invention: 1. A method for determining ubiquitin chain length was developed and this method was named ubiquitin protection from trypsinization (Ub-ProT). 2. Using Ub-ProT, it was determined that the mean length of substrate-attached ubiquitin chains is in the dimer to decamer range. 3. By quantitative proteomics, it was found that the mean lengths of five major types of ubiquitin chains can be divided into two groups. 4. Proteasome-inhibition did not alter the mean length of substrate-attached polyubiquitin chains, indicating that cells have a robust system for regulating ubiquitin chain length.