Macromolecule analysis employing nucleic acid encoding

Abstract

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

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.