Methods of polypeptide identification, and compositions therefor

Patent metadata

Field	Value
Publication number	US-2016334394-A9
Application number	US-201314100518-A
Country	US
Kind code	A9
Filing date	Dec 9, 2013
Priority date	Feb 13, 2006
Publication date	Nov 17, 2016
Grant date	—

Abstract

Methods are disclosed for identifying one or more proteins or polypeptides comprised by a sample. The methods comprise determining binding of each polypeptide with respect to each binding pool of a plurality of binding pools, wherein each binding pool comprises one or more probes which bind a structure comprised by a protein or polypeptide. In some aspects, polypeptides can be denatured and separated into individual polypeptide strands and immobilized on a solid support prior to determining binding of the binding pools. A protein, polypeptide or polypeptide strand can be identified by searching, in at least one database, for a protein or polypeptide sequence comprising binding pool targets either identical to or most similar to the binding pool targets comprised by the protein, polypeptide or polypeptide strand to be identified. Kits for identifying proteins, polypeptides and polypeptide strands are also disclosed.

First claim

What is claimed is:

1 . A method of identifying a protein or polypeptide, the method comprising:
determining presence or absence, in a protein or polypeptide to be identified, of each binding pool target of a plurality of binding pool targets, wherein each binding pool target comprises one or more binding targets for one or more probes comprised by a binding pool wherein each binding pool comprises a plurality of probes, and binds a binding pool target comprised by a population of proteins or polypeptides described in a database; and identifying, in at least one database, a protein or polypeptide comprising binding pool targets most similar to the binding pool targets comprised by the protein or polypeptide to be identified.

2 . The method of claim 1 , wherein the identified protein or polypeptide of the at least one database comprises binding pool targets identical to the binding pool targets comprised by the protein or polypeptide to be identified.

3 . The method of claim 1 , wherein a binding target of a probe comprised by a binding pool comprises a structure selected from the group consisting of a peptide motif comprising at least one amino acid up to about six amino acids, a glycosyl moiety of a glycopeptide or glycoprotein, a GPI anchor, a disulfide linkage, a pyroglutamic acid, a nitrotyrosine and a combination thereof.

4 . The method of claim 1 , wherein determining presence or absence, in the protein or polypeptide to be identified, of each binding pool target of a plurality of binding pool targets comprises:
a) contacting the protein or polypeptide to be identified sequentially or simultaneously with each binding pool of the plurality of binding pools; and b) for each binding pool, detecting binding of at least one probe comprised by the binding pool to at least one binding target if the at least one binding target is comprised by the protein or polypeptide to be identified.

5 . The method of claim 4 , wherein the plurality of binding pools comprises at least about 10 binding pools.

6 . The method of claim 1 , wherein the at least one database is a protein database comprising at least about 90% of the polypeptide sequences expressed by a species.

7 . The method of claim 6 , wherein the at least one database comprises polypeptide sequences of a mammalian proteome.

8 . The method of claim 4 , wherein each probe is selected from the group consisting of at least one antibody, at least one aptamer, at least one kinase, at least one avimer and any combination thereof.

9 . The method of claim 4 , wherein detecting binding of at least one probe comprised by the binding pool comprises detecting a label bound directly or indirectly to the at least one probe.

10 . The method of claim 4 , further comprising:
a) assigning a digital signature to the protein or polypeptide to be identified with respect to binding of the binding pools, wherein the digital signature is derived from the presence or absence of binding pool targets in the protein or polypeptide to be identified, and b) identifying a sequence comprised by at least one database having a digital signature that is identical to or has the shortest Hamming distance to the digital signature of the protein or polypeptide.

11 . The method of claim 4 , further comprising denaturing the protein or polypeptide to be identified.

12 . The method of claim 1 wherein two or more proteins or polypeptides in a sample are each identified, the method further comprising separating the two or more proteins or polypeptides in the sample.

13 . The method of claim 12 , wherein separating the two or more proteins or polypeptides in the sample comprises separating the proteins or polypeptides by electrophoresis, chromatography, or any combination thereof.

14 . The method of claim 13 , wherein the method further comprises immobilizing the proteins or polypeptides on a solid support.

15 . The method of claim 4 , wherein each binding pool of the plurality of binding pools is immobilized at an individual locus on a solid support.

16 . The method of claim 1 , wherein a protein or polypeptide to be identified is a polypeptide strand, the method further comprising:
immobilizing, on a solid support, a plurality of polypeptide strands comprised by a sample, such that each polypeptide strand to be analyzed is separated by an optically resolvable distance from other polypeptide strands comprised by the sample; wherein determining the presence or absence of each binding pool target of a plurality of binding pool targets is performed for each polypeptide strand to be analyzed; and wherein each binding pool target is a binding target for one or more probes comprised by a binding pool.

17 . The method of claim 16 , wherein the solid support comprises (i) a reactive moiety which covalently binds the polypeptide strands and/or (ii) an optically transparent medium selected from the group consisting of glass and non-fluorescent plastic.

18 . The method of claim 16 , wherein immobilizing the polypeptide strands comprises (i) covalently coupling the polypeptide strands to the solid support and/or (ii) contacting the polypeptides with a surface of the solid support, and coating the surface with a porous gel.

19 . The method of claim 16 , further comprising quantifying the polypeptide strands comprising the same or substantially the same (i) binding pool targets or (ii) digital signatures, wherein a digital signature of a polypeptide strand is derived from the presence or absence of binding pool targets in the polypeptide strand.

20 . The method of claim 16 , wherein the optically resolvable distance is about 0.5 micron or greater.

Assignees

• Mitra Robi D
• Univ Washington

Inventors

• Mitra Robi D

Classifications

• G01N33/6845 Primary

  Methods of identifying protein-protein interactions in protein mixtures · CPC title

• G01N33/582

  with fluorescent label · CPC title

• G01N33/54306 Primary

  Solid-phase reaction mechanisms · CPC title