Abstract: The present disclosure provides a method of processing an analyte, including steps of (a) providing an analyte including an epitope and a docker; (b) providing an affinity reagent, wherein the affinity reagent includes a paratope that recognizes the epitope and a tether that recognizes the docker; and (c) contacting the analyte with the affinity reagent, whereby the affinity reagent associates with the analyte via binding of the paratope to the epitope and via binding of the tether to the docker. Optionally, the method further includes the step of (d) detecting association of the affinity reagent with the analyte, thereby identifying the analyte.

Abstract: Methods and systems are provided for accurate and efficient identification and quantification of proteins. In an aspect, disclosed herein is a method for identifying a protein in a sample of unknown proteins, comprising receiving information of a plurality of empirical measurements performed on the unknown proteins; comparing the information of empirical measurements against a database comprising a plurality of protein sequences, each protein sequence corresponding to a candidate protein among a plurality of candidate proteins; and for each of one or more of the plurality of candidate proteins, generating a probability that the candidate protein generates the information of empirical measurements, a probability that the plurality of empirical measurements is not observed given that the candidate protein is present in the sample, or a probability that the candidate protein is present in the sample; based on the comparison of the information of empirical measurements against the database.

Abstract: Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.

Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.

Abstract: 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.

Abstract: Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.

Abstract: An affinity reagent, including (a) an artificial polymer comprising a branched chain; (b) an affinity moiety attached to the artificial polymer; and (c) a label attached to the artificial polymer. Also provided are methods for making and using the affinity reagent.

Abstract: The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.

Abstract: A method, including (a) providing an array of extant glycans or glycoconjugates, wherein the array comprises a plurality of addresses, wherein different extant glycans or glycoconjugates are attached to different addresses of the array; (b) contacting the array with a plurality of different probes, the different probes recognizing different carbohydrate moieties; (c) detecting positive recognition outcomes of the plurality of different probes at individual addresses of the array, thereby producing outcome profiles for the addresses; (d) providing a database comprising a set of candidate glycans or glycoconjugates, the database comprising, for each candidate glycan or glycoconjugate, the probability of a positive recognition outcome for the plurality of different probes; and (e) determining with a computer, using the database and the outcome profiles, candidate glycans or glycoconjugates in the database corresponding to different extant glycans or glycoconjugates in the array.

Abstract: Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.

Abstract: A set of polypeptides including a plurality of different polypeptides, each of the different polypeptides including a non-naturally occurring amino acid sequence, wherein a set of different epitopes occurs in the set of polypeptides, each of the different epitopes occurring in the non-naturally occurring amino acid sequence of a subset of the different polypeptides, and the non-naturally occurring amino acid sequence of each of the different polypeptides including a plurality of different epitopes of the set of epitopes.

Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.

Abstract: An affinity reagent, having: (a) a retaining component such as a structured nucleic acid particle; and (b) one or both of (i) one or more label components attached to the retaining component, and (ii) one or more binding components attached to the retaining component.

Abstract: Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.

Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.

Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.

Abstract: 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.

Abstract: The present disclosure provides methods, compositions and apparatus for generating probes having affinity for analytes of interest, such as polypeptides. Also provided are methods, compositions and apparatus for evaluating and characterizing probes.

Abstract: The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.

Abstract: Disclosed are systems and methods for identifying the binding characteristics of a partially characterized or completely unknown affinity reagent, such as an antibody or aptamer, by binding that affinity reagent against an array of known proteins. The proteins on the array which bind to the partially characterized or completely unknown affinity reagent are then determined and an analysis performed to determine the binding characteristics of the affinity reagent.