Abstract: The present disclosure provides methods for molecular neighborhood detection of molecules, such as by iterative proximity ligation or split-and-pool methods for obtaining positional information.

Abstract: The present disclosure provides methods, systems, and/or kits for analyzing a polypeptide. The method and systems may comprise a native protein coupled to a support, wherein the native protein comprises one or more internal amino acids and one or more external amino acids, and wherein the native protein comprises one or more labels coupled to said one or more external amino acids.

Abstract: Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides comprising unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Abstract: The present disclosure provides a range of methods for dense information storage in oligomeric constructs, such as peptides. Various methods of the present disclosure provide for information storage in oligomers and oligomer libraries, and information retrieval by subsequent oligomer sequencing or analysis. The present disclosure further provides methods for appending information to materials and molecules with analyzable oligomeric constructs.

Abstract: Methods and compositions for partitioning and analyzing cells are provided herein. The partitioning methods include encapsulating single cells in droplets, enabling biomolecule analysis at the single cell level. Further to this concept, multiple biomarkers can be quantified from single red blood cells, including methods which may determine whether a subject has undergone autologous blood transfer.

Abstract: Provided herein are methods for analyzing polypeptides and polypeptide complexes. Methods of the present disclosure may be used to identify protein subunits present in a polypeptide, polypeptide complex, or aggregate. These methods may also be used to quantify the subunits (e.g. number of repeating units, protein monomers, repeating domains) in a polypeptide, polypeptide complex, or aggregate.

Abstract: Provided herein are compositions, systems, methods, and kits for peptide analysis, including peptide sequencing. Aspects of the present disclosure provide bifunctional reagents which may selectively couple to amino acids and selectively couple to detectable species. Aspects of the present disclosure further provide methods for using these bifunctional reagents to sequence and analyze peptides.

Abstract: Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides comprising unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Abstract: The present disclosure provides methods of identifying and quantifying the peptides displayed by the major histocompatibility complex (MHC). Such methods may comprise the ability to determine the type, identity, and quantity of each peptide displayed by the MHC. In some embodiments, these methods may be used to develop an anti-cancer therapy or type the HLA of a patient. Also provided herein are compositions comprising peptides from the MHC which have been prepared for sequencing.

Abstract: Described herein are methods for selectively cleaving the C-terminal amino acid of a peptide or protein. The methods described herein may be applicable for, for example, single-molecule peptide or protein sequencing.

Abstract: Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides with unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Abstract: The present invention relates to methods for identifying amino acids in peptides. In one embodiment, the present invention contemplates labeling the N-terminal amino acid with a first label and labeling an internal amino acid with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Abstract: Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides comprising unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Abstract: Provided herein are rapid and reversible methods to non-specifically immobilize peptides and proteins irrespective of their sequence, as well as small molecules, on a solid support to allow for manipulations of and reactions with these molecules in a manner that does not require purification between steps, which increases sample yield and reduces the quantity of starting material required.

Abstract: The disclosure concerns methods for identifying amino acids in peptides, including peptides including unnatural amino acids. Various aspects of the present disclosure provide compositions and methods for amino acid-type specific labeling, as well as methods for detecting the labels. Further disclosed herein are strategies for highly multiplexed, high-throughput peptide analysis.

Abstract: The present invention relates to methods for identifying amino acids in peptides. In one embodiment, the present invention contemplates labeling the N-terminal amino acid with a first label and labeling an internal amino acid with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Abstract: The present disclosure provides methods of identifying and quantifying the peptides displayed by the major histocompatibility complex (MHC). Such methods may comprise the ability to determine the type, identity, and quantity of each peptide displayed by the MHC. In some embodiments, these methods may be used to develop an anti-cancer therapy or type the HLA of a patient. Also provided herein are compositions comprising peptides from the MHC which have been prepared for sequencing.

Abstract: The present disclosure provides methods of selectively label an amino acid residue on a peptide by replacing a post translational modification with a labeling moiety and sequencing the peptide to obtain the location of the amino acid residue and the identity of the post translational modification. In some aspects, the disclosure also provides methods of identifying the position, quantity, the identity of a post translational modification, or any combination thereof, in peptides which may be used for therapeutic purposes.

Abstract: The present disclosure provides methods for molecular neighborhood detection of molecules, such as by iterative proximity ligation or split-and-pool methods for obtaining positional information.

Abstract: Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides with one or more unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.