CHARACTERIZATION AND LOCALIZATION OF PROTEIN MODIFICATIONS
A method for characterizing proteins, including steps of (a) detecting a plurality of proteins, wherein individual proteins of the plurality are associated with unique identifiers, wherein the detecting distinguishes the identities of the individual proteins and the unique identifiers associated with the individual proteins; (b) digesting the proteins to form peptides, wherein the peptides from each protein are associated with the unique identifiers for the respective individual protein; (c) detecting the peptides and associated unique identifiers, wherein the detecting distinguishes characteristics of individual peptides, and wherein the detecting distinguishes unique identifiers associated with the individual peptides; and (d) correlating characteristics detected in step (c) with individual proteins detected in step (a) based on the unique identifiers associated with the individual proteins and the peptides.
1 . (canceled)
2 . A method of attaching a polypeptide to a nucleic acid particle, comprising:
(a) providing the nucleic acid particle, wherein the nucleic acid particle comprises two linking moieties, wherein each linking moiety of the two linking moieties comprises a first end and a second end, and wherein each linking moiety of the two linking moieties is attached to the nucleic acid particle by the first end; and
(b) attaching the second end of each linking moiety of the two linking moieties to the polypeptide.
3 . The method of claim 2 , further comprising: (c) after attaching the second end of each linking moiety of the two linking moieties to the polypeptide, cleaving the polypeptide.
4 . The method of claim 3 , wherein, after cleaving the polypeptide, a first linking moiety of the two linking moieties is attached to a first polypeptide fragment and a second linking moiety of the two linking moieties is attached to a second polypeptide fragment.
5 . The method of claim 4 , wherein the first polypeptide fragment comprises a post-translational modification, and wherein the second polypeptide fragment does not comprise the post-translational modification.
6 . The method of claim 2 , wherein the second end of a linking moiety of the two linking moieties comprises a reactive functional group.
7 . The method of claim 6 , wherein attaching the second end of each linking moiety of the two linking moieties to the polypeptide comprises coupling the reactive functional group of the linking moiety to a complementary reactive functional group of the polypeptide.
8 . The method of claim 2 , further comprising coupling the nucleic acid particle to a solid support.
9 . The method of claim 8 , wherein the solid support comprises a glass, a ceramic, a metal, a silica-based material, or a polymer.
10 . The method of claim 8 , wherein the solid support comprises a bead.
11 . A method of attaching a polypeptide to a first nucleic acid particle, comprising:
(a) providing the first nucleic acid particle, wherein the first nucleic acid particle is attached to a first linking moiety and a second linking moiety, wherein the first linking moiety comprises a first unique identifier label and the second linking moiety comprises a second unique identifier label, and wherein the first unique identifier label is the same as the second unique identifier label; and
(b) attaching the first linking moiety and the second linking moiety to the polypeptide.
12 . The method of claim 11 , wherein the first unique identifier or the second unique identifier label comprises a nucleic acid tag or a peptide tag.
13 . The method of claim 11 , further comprising: (c) after attaching the two linking moieties to the polypeptide, cleaving the polypeptide.
14 . The method of claim 13 , wherein, after cleaving the polypeptide, a first linking moiety of the two linking moieties is attached to a first polypeptide fragment and a second linking moiety of the two linking moieties is attached to a second polypeptide fragment.
15 . The method of claim 14 , wherein the first polypeptide fragment comprises a post-translational modification, and wherein the second polypeptide fragment does not comprise the post-translational modification.
16 . The method of claim 14 , further comprising detaching the first linking moiety and the second linking moiety from the nucleic acid particle, wherein the first linking moiety is attached to the first polypeptide fragment, and wherein the second linking moiety is attached to the second polypeptide fragment.
17 . The method of claim 16 , further comprising, after detaching the first linking moiety and the second linking moiety from the nucleic acid particle, attaching the first linking moiety to a second nucleic acid particle, and attaching the second linking moiety to a third nucleic acid particle.
18 . The method of claim 17 , further comprising attaching the second nucleic acid particle and the third nucleic acid particle to a solid support.
19 . A method of detecting a polypeptide, comprising:
(a) providing a nucleic acid particle attached to a polypeptide by two linking moieties, wherein each linking moiety of the two linking moieties comprises a first end and a second end, wherein each linking moiety of the two linking moieties is attached to the nucleic acid particle by the first end, and wherein each linking moiety of the two linking moieties is attached to the polypeptide by the second end;
(b) binding an affinity reagent to the polypeptide, wherein the affinity reagent comprises a detectable label; and
(c) after binding the affinity reagent to the polypeptide, detecting a signal from the detectable label, thereby detecting the polypeptide.
20 . The method of claim 19 , wherein binding the affinity reagent to the polypeptide comprises binding the affinity reagent to an epitope of the polypeptide comprising a post-translational modification.
21 . The method of claim 20 , wherein binding the affinity reagent to the polypeptide comprises binding the affinity reagent to an epitope of the polypeptide that does not comprise a post-translational modification.