Macromolecule analysis employing nucleic acid encoding

A method for analyzing a peptide, comprising:

• (a) contacting the peptide or a component of the peptide with a plurality of binding agents each capable of binding to the peptide or the component of the peptide, wherein the peptide or the component of the peptide is associated with a nucleic acid recording tag comprising a barcode for the peptide, and wherein each of the plurality of binding agents comprises a nucleic acid coding tag comprising an encoder sequence that comprises identifying information regarding the binding agent;
• (b) following binding between a binding agent of the plurality of binding agents and the peptide or the component of the peptide, allowing transfer of sequence information of the encoder sequence and/or the barcode for the peptide by ligation and/or primer extension between the nucleic acid coding tag of the binding agent and the nucleic acid recording tag of the peptide or the component of the peptide, thereby generating an extended nucleic acid construct comprising sequence information of the encoder sequence and the barcode for the peptide;
• (c) repeating steps (a)-(b) to perform one or more additional binding cycles for the peptide or another component of the peptide;
• and
• (d) analyzing the extended nucleic acid constructs generated during steps (a)-(c), wherein the analyzing comprises a nucleic acid sequencing, and obtaining the identifying information regarding the binding agents bound to the peptide and/or to the components of the peptide during each binding cycle, thereby analyzing the peptide.