Provided herein, in some embodiments, are methods and compositions for protein identification.

Methods and kits for evaluating a subject for a brain injury are described. The method may include providing at least one biological sample from the subject having or suspected of having the brain injury. The method may include conducting one or more amplification reactions, including contacting a portion of the biological sample with a monomeric, folded tau protein to form an incubation mixture. Each amplification reaction may include determining a presence or amount of the misfolded tau protein in the biological sample according to the amplified portion of the misfolded tau protein. Methods for evaluating the risk of neurodegenerative disease or disorder in a subject having suffered from brain injury are also described.

The present disclosure provides treatment modalities, e.g., strategies, treatment methods, patient stratification methods, combinations, and compositions that are useful for the treatment of disorders, e.g., proliferative disorders, such as certain cancer. Some aspects of this disclosure provide treatment modalities, methods, strategies, compositions, combinations, and dosage forms for the treatment of cell proliferative disorders, e.g., cancers, dependent upon EZH2 (enhancer of zeste 2 polycomb repressive complex 2) function with an EZH2 inhibitor.

The present description provides methods, assays and reagents useful for sequencing proteins. Sequencing proteins in a broad sense involves observing the plausible identity and order of amino acids, which is useful for sequencing single polypeptide molecules or multiple molecules of a single polypeptide. In one aspect, the methods are useful for sequencing multiple polypeptides. The methods and reagents described herein can be useful for high resolution interrogation of the proteome and enabling ultrasensitive diagnostics critical for early detection of diseases.

The present disclosure provides a method of identifying a polypeptide. The method can include steps of (a) attaching a polypeptide to a particle or solid support, thereby producing an immobilized polypeptide having a plurality of amino acids linked to the particle or solid support; (b) fragmenting the immobilized polypeptide, whereby the particle is attached to a set of fragments of the polypeptide; (c) performing a binding assay including contacting the set of fragments with a plurality of affinity reagents and detecting binding of affinity reagents of the plurality of affinity reagents to the set of fragments; and (d) identifying the polypeptide from results of the binding assay.

A screening method for an amino acid sequence of a protein nanopore, a protein nanopore, and applications thereof. The screening method includes: evaluating a characteristic sequence of a dual-pore structure, using a model to search for an amino acid sequence matched with the characteristic feature of the dual-pore structure, removing a redundant candidate sequence and then performing positioning and screening, calculating the matching length and envelope length of the candidate sequence, then performing registration to obtain a relative mismatching relationship with a known protein nanopore, and performing analysis to obtain a final sequence.

The present invention is methods and assays for identifying single proteins from a sample, without the use of affinity reagents. The methods and assays combine endopeptidase-based component of conventional peptide mapping with single molecule labeling and a microreactor array platform. The invention also includes kits for performing the methods and assays.

Provided is a method for efficiently searching a peptide library for an oligopeptide that can be bound to the end of a protein or peptide of interest. Further, provided is an efficient and highly safe immunoassay.

The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.

Systems and methods for determining amino acid sequences of peptides that bind to MHC-I or HLA-I complex or MHC-II or HLA-II complex are provided. One embodiment includes isolating peptides from MHC or HLA class I or class II-peptide complexes and adding one or more known labeled peptides of interest to form a sample containing labeled peptides and unlabeled isolated peptides. The method also includes analyzing the sample with an LC-MS/MS system to obtain sequence data of the peptides, and increasing the sensitivity of the LC-MS/MS system when the labeled peptide is detected by the LC-MS/MS system. The method then concludes with determining the amino acid sequence of the unlabeled peptides in an m/z range that includes the m/z of the labeled peptide. The system can be triggered to increase the sensitivity in or near the m/z of the labeled peptide using an algorithm or computer program.