Characterization and localization of protein modifications

An array comprising a first address for binding a first polypeptide and a second address for binding a second polypeptide, wherein the first address and the second address are optically resolvable, wherein the first address is attached to a first nucleic acid particle, wherein the second address is attached to a second nucleic acid particle, and wherein:

• a) the first nucleic acid particle comprises two or more linking moieties, wherein the two or more linking moieties of the first nucleic acid particle are attached to the first polypeptide;
• and
• b) the second nucleic acid particle comprises two or more linking moieties, wherein the two or more linking moieties of the second nucleic acid particle are attached to the second polypeptide;
• wherein the first polypeptide differs from the second polypeptide.

A system comprising:

• a) a solid support, wherein an address of the solid support is attached to a nucleic acid particle, wherein the particle comprises two or more linking moieties, wherein the two or more linking moieties of the nucleic acid particle are attached to a polypeptide;
• b) a detectable affinity reagent, wherein the detectable affinity reagent is configured to provide a detectable signal, and wherein the detectable affinity reagent is configured to be delivered to the solid support;
• c) an optical detector;
• and
• d) one or more processors programmed to read data from the optical detector to detect a presence or absence of the detectable signal at the address of the solid support.