Methods of analyzing glycosylated biomolecules include the steps of producing a deglycosylation mixture of biomolecules deglycosylated by natural or synthetic enzymatic or chemical techniques; providing a reagent solution having a labeling reagent in a polar aprotic, non-nucleophilic organic solvent; and mixing the deglycosylation mixture with the reagent solution in an excess of labeling reagent to produce derivatized glycosylamines. The method steps can be carried out purposefully without depletion of protein matter. A quenching solution can be added to the reaction mixture so that the pH of the reaction mixture is shifted to above 10. The yield of derivatized glycosylamines can be in an amount of about 80 to about 100 mole percent of the reaction mixture with minimal overlabeling, less than 0.2 mole percent. The derivizated glycosylamines can be separated from the reaction mixture and detected by chromatographic detection, fluorescence detection, mass spectrometry (MS), or Ultra Violet (UV) detection and/or a combination thereof.

Provided herein are several methods for selecting agents that bind to transmembrane receptors in a conformationally-selective way. In some embodiments, the method may comprise producing: a transmembrane receptor in an active conformation; and said transmembrane receptor in an inactive conformation and using cell sorting to select, from a population of cells comprising a library of cell surface-tethered extracellular capture agents, cells that are specifically bound to either the transmembrane receptor in its active conformation or the transmembrane receptor in its inactive conformation, but not both. In other embodiments, the method may comprise: contacting a GPCR with a population of cells that comprise a library of surface-tethered extracellular proteins; labeling the cell population with a conformationally-specific binding agent, e.g., a G-protein or mimetic thereof; and using cell sorting to select from the cell population cells that bind to the agent.

Methods and kits for enzymes involved in post-translational modifications are provided. The methods employ elemental analysis, including ICP-MS. The methods allow for the convenient and accurate analysis of post-translation modifications of substrates by enzymes involved in post-translational modifications, including kinase and phosphatase enzymes. Kits may include an element tag for directly tagging an affinity product that recognizes phosphorylated substrates, as well as a non-phosphorylated substrate or an expression plasmid.

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.

Some embodiments relate to nanoparticle probes for the detection of disease states in a patient or for tissue engineering. In some embodiments, the nanoparticle probe comprises one or more slip bonds that bind to a cell surface structure. In some embodiments, the binding of the nanoparticle probe is selective. In some embodiments, the nanoparticle probe binds to cells having a certain maximum glycocalyx thickness.

Disclosed is a proteomic reactor, comprising a pipette tip, an ion exchange resin filler and a solid-phase extraction membrane. The solid-phase extraction membrane is filled into the lower end of the pipette tip, and the ion exchange resin is filled into the lower end of the pipette tip and is located above the solid-phase extraction membrane. The ion exchange resin is a strong cation exchange resin or a strong anion exchange resin. Disclosed is a protein chromatographic separation platform comprising the proteomic reactor and a liquid chromatography-mass spectrometer. Disclosed is the use of the proteomic reactor and protein chromatographic separation platform in the protein identification and protein quantitative analysis of a cell, a tissue or a blood sample.

A hemoglobin species determination method includes preparing a trained model generated by using, as a learning data set for machine learning, a data set including learning frequency analysis data generated by performing frequency analysis on separation data generated by a separation process on a learning blood sample in which a species of hemoglobin is known and including the known species of hemoglobin, preparing test frequency analysis data by performing frequency analysis on separation data generated by a separation process on a test blood sample in which the species of hemoglobin is unknown, and determining the species of hemoglobin contained in the test blood sample by inputting the test frequency analysis data to the trained model.

The present disclosure relates to method of detecting proteins proximal to a target protein using fusion proteins which include: a glycan binding component linked to a mutant E. coli biotin ligase BirA, the glycan binding component capable of specific binding to a glycosylation post-translational modification of a target protein and the mutant E. coli biotin ligase BirA having enzymatic activity to ligate biotin to proteins proximal to the target protein. Such methods include contacting a living cell with the fusion protein under compatible biological conditions, whereby the fusion protein specifically binds to a glycosylation post-translational modification of a target protein of the cell; providing biotin to the living cell, whereby the mutant E. coli biotin ligase BirA ligates biotin to proteins proximal to the target protein; and detecting the biotinylated proteins, thereby detecting proteins proximal to the target protein.

The present invention provides compositions and methods that can be used to determine a peptide signature for an antibody repertoire in a sample comprising multiple antibodies. The method can be used to characterize a phenotype in a sample, such as providing a diagnosis, prognosis or theranosis of a medical condition.

Systems and methods for obtaining qualitative or quantitative measurements of proteoforms of polypeptides are described. The described methods include measurements of affinity reagent binding on single-molecule polypeptide arrays to distinguish between polypeptide isoforms. The described methods may provide high resolution quantitative comparisons of proteoforms with very low copy numbers.