Global Proteomic screening of random bead arrays using mass spectrometry imaging

• US 9,523,680 B2
• Filed: 06/29/2011
• Issued: 12/20/2016
• Est. Priority Date: 06/30/2010
• Status: Active Grant

• Current Assignee: Ambergen Inc.
• Original Assignee: Ambergen Inc.
• Inventors: Lim, Mark J., Bergo, Vladislav B., Rothschild, Kenneth J.
• Primary Examiner(s): Cheu, Jacob
• Application Number:
  US13/172,164
• Publication Number:
  US 20120077688A1
• Time in Patent Office: 2,001 Days
• Field of Search: 506/7
• US Class Current: 1/1
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry

Abstract

Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

Claims

1. A label-free method of detecting the interaction of prey molecules with bait molecules on an array of beads, comprising:

a) providing a mixture comprising first and second beads, said first beads comprising first bait molecules and said first beads having a first mass tag attached, said second beads comprising second bait molecules and said second beads having a second mass tag attached, wherein said first and second bait molecules and said first and second mass tags are different;

b) contacting said first and second beads with a solution comprising a population of prey molecules;

c) making an array with said beads, imaging said beads in said array; and

d) subjecting said array to mass spectrometry analysis under conditions wherein at least one of said first and second beads is identified by detection of its corresponding mass tag, and wherein the at least one of said first or second identified beads had bound to said prey molecules, wherein said mass spectrometry analysis comprises imaging of individual beads in said array.

2. The method of claim 1, wherein said mass tags are selected from the group consisting of polypeptides, nucleic acids, linear polymers, and branched polymers.

3. The method of claim 1, wherein said mass tags are released by light and detected during the mass spectrometry analysis of step d).

4. The method of claim 1, wherein said first and second mass tag are coupled to said first and second beads through a binding agent.

5. The method of claim 4, wherein said binding agent is streptavidin.

6. The method of claim 1, wherein said prey molecule is an antibody.

7. The method of claim 1, wherein said prey molecule is a protein.

8. The method of claim 1, wherein said prey molecule is a polypeptide.

9. The method of claim 1, wherein said prey molecule is a nucleic acid.

10. The method of claim 1, wherein said prey molecule is a small drug compound.

11. The method of claim 1, wherein said prey molecules comprise a third mass tag which is different than said first and second mass tags, said third mass tag coupled to said prey molecule through a binding agent.

12. The method of claim 11 wherein said binding agent is an antibody.

13. The method of claim 1, wherein said mass spectrometry analysis in step d) comprises measuring mass tags from individual beads.

14. The method of claim 1, wherein said array of step c) is a random array.

15. A label-free method of detecting the interaction of prey molecules with bait molecules, comprising:

a) providing a mixture comprising first and second beads, said first beads comprising first bait molecules and said first beads having a first mass tag attached, said second beads comprising second bait molecules and said second beads having a second mass tag attached, wherein said first and second bait molecules and said first and second mass tags are different;

b) making an array with said beads;

c) contacting said beads with a solution comprising a population of prey molecules, imaging said beads in said array; and

d) subjecting said array to mass spectrometry analysis under conditions wherein at least one of said first and second beads is identified by detection of its corresponding mass tag, and wherein the at least one of said first or second identified beads had bound to said prey molecules, wherein said mass spectrometry analysis comprises imaging of individual beads in said array.

16. The method of claim 15, wherein said mass tags are selected from the group consisting of polypeptides, nucleic acids, linear polymers, and branched polymers.

17. The method of claim 15, wherein said mass tags are released by light and detected during the mass spectrometry analysis of step d).

18. The method of claim 15, wherein said first and second mass tag are coupled to said first and second beads through a binding agent.

19. The method of claim 18, wherein said binding agent is streptavidin.

20. The method of claim 15, wherein said prey molecule is an antibody.

21. The method of claim 15, wherein said prey molecule is a protein.

22. The method of claim 15, wherein said prey molecule is a polypeptide.

23. The method of claim 15, wherein said prey molecule is a nucleic acid.

24. The method of claim 15, wherein said prey molecule is a small drug compound.

25. The method of claim 15 wherein said prey molecules comprise a third mass tag which is different than said first and second mass tags, said third mass tag coupled to said prey molecule through a binding agent.

26. The method of claim 25 wherein said binding agent is an antibody.

27. The method of claim 15, wherein said mass spectrometry analysis in step d) comprises measuring mass tags from individual beads.

28. The method of claim 15, wherein said array of step d) is a random array.