Global proteomic screening of random bead arrays using mass spectrometry imaging

• US 9,513,285 B2
• Filed: 12/17/2013
• Issued: 12/06/2016
• 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:
  US14/108,641
• Publication Number:
  US 20140235471A1
• Time in Patent Office: 1,085 Days
• Field of Search: None
• 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 method of detecting the interaction of prey molecules with bait molecules on an array of beads, comprising:

a. providing i) a mixture comprising first and second beads, said first beads comprising first bait molecules, said second beads comprising second bait molecules, wherein said first and second bait molecules are different; and

ii) prey molecules, wherein said prey molecules comprise a detectable label;

b. contacting said first and second beads with a solution comprising a population of said prey molecules under conditions wherein said prey molecules can bind to a bait molecule;

c. making a random array with said beads by depositing a mixture of said first and second beads onto a solid surface;

d. imaging said beads in said array for the presence of said detectable label to detect interaction of prey molecules with bait molecules; and

e. subjecting said array directly to mass spectrometry measurements under conditions such that one or more individual beads detected by the imaging in step d) are also detected in the same location within the array by said mass spectrometry measurements, wherein said mass spectrometry measurements detect said bait molecules or fragments thereof from said individual beads, individually resolving said beads and allowing identification of said beads in said imaged array.

2. The method of claim 1, wherein said detectable labels are fluorescent labels, radioisotope labels, mass-tag labels, chemiluminescent labels, antibody labels, secondary antibody labels, or enzymatic labels.

3. The method of claim 1, wherein said imaging of said beads in said array in step d) comprises the methods of fluorescence, radioisotopes, absorption, luminescence, Raman, or infrared.

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

5. The method of claim 1, wherein said prey molecules are proteins.

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

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

8. A method of detecting the interaction of prey molecules with bait molecules on an array of beads, comprising:

a. providing i) a mixture comprising first and second beads, said first beads comprising first bait molecules, said second beads comprising second bait molecules, wherein said first and second bait molecules are different;

ii) prey molecules; and

iii) detectable labels capable of being coupled to said prey molecules;

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

c. contacting said first and second beads with a second solution comprising said detectable labels;

d. making a random array with said beads by depositing a mixture of said first and second beads onto a solid surface;

e. imaging said beads in said array for the presence of said detectable labels; and

f. subjecting said array directly to mass spectrometry measurements under conditions such that one or more individual beads detected by the imaging in step e) are also detected in the same location within the array by said mass spectrometry measurements, wherein said mass spectrometry measurements detect said bait molecules or fragments thereof from said individual beads, individually resolving said beads and allowing identification of said beads in said imaged array.

9. The method of claim 8, wherein said prey molecules comprise antibodies in serum and said second solution of step c) comprises secondary antibodies comprising detectable labels and reactive with said antibodies in serum.

10. The method of claim 8, wherein said detectable labels are fluorescent labels, radioisotope labels, mass tag labels, chemiluminescent labels, antibody labels, secondary antibody labels, or enzymatic labels.

11. The method of claim 8, wherein said imaging of said beads in said array in step e) comprises the methods of fluorescence, radioisotopes, absorption, luminescence, Raman, or infrared.

12. The method of claim 8, wherein said detectable labels are coupled to said prey molecules by antibodies, avidin, streptavidin, or avidin/streptavidin derivatives capable of binding biotin.

13. A method of making and decoding an array, comprising:

a) providing i) a mixture comprising first and second beads, said first beads comprising first bait molecules, said second beads comprising second bait molecules, wherein said first and second bait molecules are different, and wherein at least one of said first and second beads comprises a detectable label; and

ii) a surface;

b) making a random array of said beads by depositing a mixture of said first and second beads on said surface;

c) imaging said array to detect the presence of said detectable label; and

d) subjecting said array directly to mass spectrometry analysis under conditions wherein the identity of said bait on at least a portion of said beads is determined by said mass spectrometry analysis of said bait or fragments thereof, wherein said mass spectrometry measurements detect individually resolved beads, and wherein at least a portion of individual beads identified by said mass spectrometry analysis are also detected in the same location within the array by said imaging in step c).

14. The method of claim 13, wherein said imaging of said array in step c) comprises the methods of fluorescence, radioisotopes, absorption, luminescence, Raman, or infrared.