Methods and compositions for protein and peptide sequencing

1. A method of identifying one or more binding events between a plurality of binders and a plurality of binding targets, comprising:

(a) incubating a plurality of known binding targets with a library of binders, where one or more binders within the library bind specifically to one or more binding targets, wherein each binder within the library comprises a target binder sequence and a unique barcode sequence indicative of the associated binder;

(b) ligating the unique barcode sequence that is specifically bound to a binding target onto a DNA barcode sequence proximal to the binding target, thereby generating a DNA barcode construct;

(c) removing the target binder sequence, thereby leaving the barcode sequence attached to the DNA barcode construct, such that the identity of the binder and, therefore, the identity of the binding target is identified;

(d) optionally, repeating steps (b)-(c);

(e) ligating sequencing adaptors onto the DNA barcode construct; and

(f) sequencing the DNA barcode construct,

thereby identifying one or more binding events between a plurality of binders and a plurality of binding targets.

2. The method of claim 1 , wherein the library of binders are selected from the group consisting of a library of aptamer binders, a library of antibody binders, and a library of small molecule binders.

3. The method of claim 1 , wherein the plurality of binding targets are selected from the group consisting of peptides, proteins, and protein complexes, lipid molecules, viruses, ultramicrobacteria, and inorganic molecules.

4. The method of claim 1 , wherein the library of binders are immobilized on a solid substrate.

5. The method of claim 4 , wherein the solid substrate is glass.

6. The method of claim 1 , wherein the plurality of binding targets are modified with a DNA barcode tail.

7. The method of claim 1 , wherein the plurality of binding targets are modified in solution.

8. The method of claim 1 , wherein, when the library of binders are a library of aptamer binders, the method further comprises ligating a sequencing adaptor to each member of the library of aptamer binders.

9. The method of claim 1 , wherein the ligating step (b) and/or the ligating step (e) is an enzymatic ligation.

10. The method of claim 1 , wherein the sequencing uses a next generation sequencing (NGS) platform.