A method of identifying of amino-acid residues on a target protein that form a binding site of a molecule of interest. Such method relies on selection of relevant patches of solvent-accessible residues and testing of an array of mutated proteins for changes of binding properties. Such method is useful for determining binding sites (epitopes) of antibodies, ligands and related molecules.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

Provided herein is an improved method of antibody affinity maturation that uses true natural CDRs from a population of naturally occurring antibodies targeting a single antigen or antigenic epitope such that the improved method produces functional antibodies having low-picomolar affinity antibodies. Also provided herein is an antibody library where the CDRs within a single antibody member of the library are a combination of CDR sequences of naturally occurring antibodies and one or more CDRs are derived from different naturally occurring antibodies targeting a single antigen or antigenic epitope.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

Compositions for use in diagnostic screens for Mycoplasma haemofelis are provided. In one embodiment an immunogenic peptide selected from SEQ ID NO: 1 to SEQ ID NO: 60, or a fragment thereof, is immobilized on a solid support and is used to detect the presence of Mycoplasma haemofelis antibodies in a patient bodily fluid. In accordance with one embodiment a method for detecting a Mycoplasma haemofelis infection in a feline species, is provided.

Compositions for use in diagnostic screens for Mycoplasma haemofelis are provided. In one embodiment an immunogenic peptide selected from SEQ ID NO: 1 to SEQ ID NO: 60, or a fragment thereof, is immobilized on a solid support and is used to detect the presence of Mycoplasma haemofelis antibodies in a patient bodily fluid. In accordance with one embodiment a method for detecting a Mycoplasma haemofelis infection in a feline species, is provided.

The present invention is useful in screening for biomarkers associated with any other disease or condition. Such diseases and conditions range from the neurological diseases, autoimmune diseases and cancers identified above as well as any other disease or condition that has a biomarker such as an antibody or other characterizing protein or biomolecule associated with the disease or progression of the disease. The large ligand libraries of the invention can be used directly in biological fluid, under the appropriate experimental conditions and according to the processes recited herein, to screen for such markers and without the need to use fewer support members (e.g. about 100,000 or less) or without the need to transfer such peptoids or ligands to a microarray before screening the biological fluid. In addition, the ligand libraries may also be used to screen for cell based receptors that specifically relate to a particular cell surface marker.

The present invention is useful in screening for biomarkers associated with any other disease or condition. Such diseases and conditions range from the neurological diseases, autoimmune diseases and cancers identified above as well as any other disease or condition that has a biomarker such as an antibody or other characterizing protein or biomolecule associated with the disease or progression of the disease. The large ligand libraries of the invention can be used directly in biological fluid, under the appropriate experimental conditions and according to the processes recited herein, to screen for such markers and without the need to use fewer support members (e.g. about 100,000 or less) or without the need to transfer such peptoids or ligands to a microarray before screening the biological fluid. In addition, the ligand libraries may also be used to screen for cell based receptors that specifically relate to a particular cell surface marker.