MACROMOLECULE ANALYSIS EMPLOYING NUCLEIC ACID ENCODING

1 - 177 . (canceled)

178 . A method for analyzing a polypeptide, the method comprising the steps of:

(a) providing the polypeptide and an associated recording tag joined to a solid support;

(b) contacting the polypeptide with a binding agent capable of binding to the polypeptide, wherein the binding agent comprises a coding tag with identifying information regarding the binding agent;

(c) transferring the information of the coding tag to the recording tag to generate an extended recording tag;

(d) analyzing the extended recording tag, thereby characterizing, identifying or quantifying all or a portion of components of the polypeptide.

179 . The method of claim 178 , wherein providing the polypeptide and the associated recording tag at step (a) comprises the steps of:

(q) partitioning a plurality of polypeptides from a sample into a plurality of compartments, wherein each compartment comprises a plurality of recoding tags optionally attached to beads, wherein each recoding tag of the plurality of recoding tags comprises a compartment tag that is the same within an individual compartment and different from the compartment tags of other compartments;

(r) contacting the partitioned polypeptides with pluralities of recording tags within the plurality of compartments under conditions sufficient to permit joining of the partitioned polypeptides to recoding tags, thereby generating a plurality of recoding tag-labeled polypeptides;

(s) optionally releasing recoding tags from the plurality of recoding tags from the beads;

(t) collecting the recoding tag-labeled polypeptides from the plurality of compartments; and

(u) immobilizing the recoding tag-labeled polypeptides on the solid support.

180 . The method of claim 178 , further comprising fragmenting the plurality of polypeptides after partitioning into the plurality of compartments to obtain fragmented polypeptides and before step (t), wherein recoding tag-labeled fragmented polypeptides are collected from the plurality of compartments and immobilized on the solid support.

181 . The method of claim 178 , wherein providing the polypeptide at step (a) comprises the steps of:

(q) partitioning a plurality of polypeptides from a sample into a plurality of compartments, wherein each compartment comprises a plurality of recoding tags attached to beads, wherein each recoding tag of the plurality of recoding tags comprises a compartment tag that is the same within an individual compartment and different from the compartment tags of other compartments;

(r) contacting the partitioned polypeptides with pluralities of recording tags within the plurality of compartments under conditions sufficient to permit joining of the partitioned polypeptides to recoding tags, thereby generating a plurality of recoding tag-labeled polypeptides;

(s) releasing recoding tags from the plurality of recoding tags from the beads;

(t) collecting the recoding tag-labeled polypeptides from the plurality of compartments; and

(u) immobilizing the recoding tag-labeled polypeptides on the solid support.

182 . The method of claim 178 , wherein at step (q) an interacting protein complex within the sample is partitioned into a compartment of the plurality of compartments, and the method provides analysis of polypeptides derived from the interacting protein complex.

183 . The method of claim 178 , wherein the binding agent binds specifically to a post-translationally modified amino acid of the polypeptide.

184 . The method of claim 183 , wherein the post-translationally modified amino acid of the polypeptide comprises phosphorylation or glycosylation.

185 . The method of claim 183 , further comprising contacting an amino acid of the polypeptide with a modifying reagent before step (b) to obtain the post-translationally modified amino acid.

186 . The method of claim 179 , wherein at step (r) the partitioned polypeptides are covalently joined to the recoding tags.

187 . The method of claim 178 , wherein the polypeptide has from 10 amino acid residues to 70 amino acid residues.

188 . The method of claim 178 , wherein analyzing the polypeptide comprises identifying a component or a portion of the polypeptide.

189 . The method of claim 178 , wherein analyzing the extended recording tag comprises a nucleic acid sequencing method.

190 . The method of claim 178 , wherein the binding agent is joined to the coding tag via a SpyCatcher-SpyTag interaction.