Global proteomic screening of random bead arrays using mass spectrometry imaging

• US 10,060,912 B2
• Filed: 10/03/2016
• Issued: 08/28/2018
• 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, Changhwa J
• Application Number:
  US15/283,694
• Publication Number:
  US 20170089891A1
• Time in Patent Office: 694 Days
• Field of Search: None
• 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 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 second beads comprising second bait molecules, wherein said first and second bait molecules are different;

b. contacting said first and second beads with a solution comprising a population of prey molecules, wherein at least a portion of said prey molecules binds to at least one of said first and second beads to create a reacted bead;

c. making an array with said beads; and

d. subjecting said array directly to mass spectrometry analysis under conditions wherein said prey from said reacted bead is detected by said mass spectrometry, wherein said mass spectrometry analysis comprises mass spectrometry imaging of individual beads in said array.

2. The method of claim 1, wherein said prey molecules are from blood, serum or plasma.

3. The method of claim 1, wherein said prey molecules are from cell lysates, tissue lysates or cell culture supernatants.

4. The method of claim 1, wherein said prey molecules are proteins or protease digested proteins.

5. The method of claim 1, wherein said prey molecules are peptides or protein fragments.

6. The method of claim 1, wherein said prey molecules are antibodies.

7. The method of claim 1, wherein said prey molecules are nucleic acids.

8. The method of claim 1, wherein said prey molecules are drugs or candidate drugs.

9. The method of claim 1, wherein said bait molecules are proteins, protein fragments or peptides.

10. The method of claim 1, wherein said bait molecules are antibodies.

11. The method of claim 1, wherein said bait molecules are drugs or candidate drugs.

12. The method of claim 1, wherein said bait molecules are nucleic acids.

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

14. A 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 second beads comprising second bait molecules, wherein said first and second bait molecules are different;

b. making an array with said beads;

c. contacting said array with a solution comprising a population of prey molecules, wherein at least a portion of said prey molecules binds to at least one of said first and second beads in said array to create reacted beads;

d. subjecting said array directly to mass spectrometry analysis under conditions wherein said prey from said reacted bead is detected by said mass spectrometry, wherein said mass spectrometry analysis comprises mass spectrometry imaging of individual beads in said array.

15. The method of claim 14, wherein said prey molecules are from blood, serum or plasma.

16. The method of claim 14, wherein said prey molecules are from cell lysates, tissue lysates or cell culture supernatants.

17. The method of claim 14, wherein said prey molecules are proteins or protease digested proteins.

18. The method of claim 14, wherein said prey molecules are peptides or protein fragments.

19. The method of claim 14, wherein said prey molecules are antibodies.

20. The method of claim 14, wherein said prey molecules are nucleic acids.

21. The method of claim 14, wherein said prey molecules are drugs or candidate drugs.

22. The method of claim 14, wherein said bait molecules are proteins, protein fragments or peptides.

23. The method of claim 14, wherein said bait molecules are antibodies.

24. The method of claim 14, wherein said bait molecules are drugs or candidate drugs.

25. The method of claim 14, wherein said bait molecules are nucleic acids.

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