MACROMOLECULE ANALYSIS EMPLOYING NUCLEIC ACID ENCODING

1 - 177 . (canceled)

178 . A nucleic acid library, which comprises information regarding a plurality of peptides, wherein the nucleic acid library comprises at least 1,000,000 nucleic acid molecules, and each nucleic acid molecule of the nucleic acid library comprises:

(i) at least three different encoder sequences or complements thereof, and

(ii) a unique molecular identifier (UMI) and/or a universal priming site for priming amplification and/or for sequencing of the nucleic acid library,

wherein each encoder sequence comprises identifying information regarding a binding agent that binds to a component of one or more peptides of the plurality of peptides.

179 . The nucleic acid library of claim 178 , wherein each of the at least 1,000,000 nucleic acid molecules are attached to a solid support.

180 . The nucleic acid library of claim 179 , wherein adjacent nucleic acid molecules on the solid support are spaced apart from each other on a surface or within a volume of the solid support at an average distance of about 50 nm or greater.

181 . (canceled)

182 . The nucleic acid library of claim 178 , wherein each nucleic acid molecule of the nucleic acid library further comprises a sample barcode.

183 . The nucleic acid library of claim 178 , wherein each nucleic acid molecule of the nucleic acid library comprises identifying information regarding a single peptide of the plurality of peptides.

184 . The nucleic acid library of claim 178 , wherein the diversity of UMI sequences exceeds the number of nucleic acid molecules in the nucleic acid library.

185 . The nucleic acid library of claim 184 , wherein the UMI distinguishes the nucleic acid molecule that comprises identifying information regarding a peptide of the plurality of peptides from nucleic acid molecules of the nucleic acid library that comprise identifying information regarding other peptides of the plurality of peptides.

186 . The nucleic acid library of claim 178 , wherein the plurality of peptides comprises at least 10,000 different peptide molecules.

187 . The nucleic acid library of claim 178 , wherein the plurality of peptides comprises at least 100,000 different peptide molecules.

188 . The nucleic acid library of claim 178 , wherein the binding agent binds to the component of one or more peptides of the plurality of peptides while being associated with the encoder sequence.

189 . The nucleic acid library of claim 178 , wherein the component of one or more peptides comprises a terminal amino acid residue of the one or more peptides.

190 . The nucleic acid library of claim 189 , wherein each of the at least three different encoder sequences corresponds to an N-terminal amino acid residue of the one or more peptides.

191 . The nucleic acid library of claim 189 , wherein each of the at least three different encoder sequences corresponds to a C-terminal amino acid residue of the one or more peptides.

192 . The nucleic acid library of claim 178 , wherein the component of one or more peptides comprises a modified terminal amino acid residue of the one or more peptides.

193 . The nucleic acid library of claim 192 , wherein each of the at least three different encoder sequences corresponds to a modified N-terminal amino acid residue of the one or more peptides.

194 . The nucleic acid library of claim 192 , wherein each of the at least three different encoder sequences corresponds to a modified C-terminal amino acid residue of the one or more peptides.

195 - 196 . (canceled)

197 . The nucleic acid library of claim 178 , wherein each of the at least three different encoder sequences corresponds to one or more amino acids selected from the group consisting of Alanine (A or Ala), Cysteine (C or Cys), Aspartic Acid (D or Asp), Glutamic Acid (E or Glu), Phenylalanine (F or Phe), Glycine (G or Gly), Histidine (H or His), Isoleucine (I or Ile), Lysine (K or Lys), Leucine (L or Leu), Methionine (M or Met), Asparagine (N or Asn), Proline (P or Pro), Glutamine (Q or Gln), Arginine (R or Arg), Serine (S or Ser), Threonine (T or Thr), Valine (V or Val), Tryptophan (W or Trp), and Tyrosine (Y or Tyr).

198 . The nucleic acid library of claim 178 , wherein each nucleic acid molecule of the nucleic acid library is obtained by transfer of an encoder sequence from a binding agent, which the encoder sequence identifies and is attached to, onto a single nucleic acid molecule upon binding of the binding agent to a component of one or more peptides of the plurality of peptides, and which transfer is performed for each encoder sequence of the at least three different encoder sequences.

199 . The nucleic acid library of claim 178 , wherein the binding agent is attached to a nucleic acid molecule of the at least 1,000,000 nucleic acid molecules.

200 . The nucleic acid library of claim 178 , wherein each nucleic acid molecule of the nucleic acid library comprises the UMI and the universal priming site.

201 . A nucleic acid library, which comprises information regarding a plurality of peptides, wherein the nucleic acid library comprises at least 1,000,000 nucleic acid molecules, and each nucleic acid molecule of the nucleic acid library comprises:

(i) at least three different encoder sequences or complements thereof, and

(ii) a unique molecular identifier (UMI) and/or a universal priming site for priming amplification and/or for sequencing of the nucleic acid library,

wherein each nucleic acid molecule of the nucleic acid library is obtained by transfer of an encoder sequence which comprises identifying information regarding a binding agent from the binding agent onto the nucleic acid molecule upon binding of the binding agent to a component of one or more peptides of the plurality of peptides, and which transfer is performed for each encoder sequence of the at least three different encoder sequences.

202 . The nucleic acid library of claim 201 , wherein each of the at least 1,000,000 nucleic acid molecules are attached to a solid support.

203 . The nucleic acid library of claim 202 , wherein adjacent nucleic acid molecules on the solid support are spaced apart from each other on a surface or within a volume of the solid support at an average distance of about 50 nm or greater.

204 . The nucleic acid library of claim 201 , wherein each nucleic acid molecule of the nucleic acid library comprises identifying information regarding a single peptide of the plurality of peptides.

205 . The nucleic acid library of claim 204 , wherein the diversity of UMI sequences exceeds the number of nucleic acid molecules in the nucleic acid library, and wherein the UMI distinguishes the nucleic acid molecule that comprises identifying information regarding a peptide of the plurality of peptides from nucleic acid molecules of the nucleic acid library that comprise identifying information regarding other peptides of the plurality of peptides.

206 . The nucleic acid library of claim 201 , wherein the plurality of peptides comprises at least 10,000 different peptide molecules.

207 . The nucleic acid library of claim 201 , wherein the component of one or more peptides comprises a terminal amino acid residue of the one or more peptides.

208 . The nucleic acid library of claim 207 , wherein each of the at least three different encoder sequences corresponds to an N-terminal amino acid residue of the one or more peptides.

209 . The nucleic acid library of claim 207 , wherein each of the at least three different encoder sequences corresponds to a C-terminal amino acid residue of the one or more peptides.

210 . The nucleic acid library of claim 201 , wherein the component of one or more peptides comprises a modified terminal amino acid residue of the one or more peptides.