Granted Patent B2

US 12,633,372 · App. 18/916,443 · Granted May 19, 2026

Inventors: Sujal M. Patel (Seattle, WA); Parag Mallick (San Mateo, CA); Jarrett D. Egertson (San Carlos, CA)

Assignee: NAUTILUS SUBSIDIARY, INC.

G16B5/20G01N27/26G01N27/60G01N27/72

Abstract

Claims (38)

1 . A method for characterizing proteins in a sample, comprising:

providing a plurality of proteins from a sample, wherein individual proteins in the plurality of proteins have a unique spatial address on a substrate;

carrying out a series of affinity binding measurements by sequentially applying a series of tagged affinity reagents to the plurality of proteins attached to the unique spatial addresses on the substrate to produce an outcome set comprising positive binding outcomes and negative binding outcomes for the individual proteins in the plurality of proteins with the tagged affinity reagents;

providing a database comprising a set of candidate proteins, and for each candidate protein, a probability of observing a positive binding outcome or negative binding outcome with each of the tagged affinity reagents;

characterizing the plurality of proteins attached to the substrate by determining with a computer, using the database comprising the set of candidate proteins and the probabilities, and the outcome set, identity information for a probable group of candidate proteins in the database corresponding to each individual protein of the plurality of proteins attached to the substrate; and

storing the characterization of each individual protein of the plurality of proteins and their corresponding unique spatial addresses on the substrate to a computer memory to characterize each of the individual proteins present in the sample.

2 . The method of claim 1 , wherein characterizing the plurality of proteins includes quantifying the candidate proteins in the plurality of proteins attached to the substrate.

3 . The method of claim 1 , wherein characterizing the plurality of proteins includes identifying the plurality of proteins attached to the substrate.

4 . The method of claim 3 , further comprising quantifying the plurality of proteins based on the identification of the plurality of proteins attached to the substrate.

5 . The method of claim 1 , wherein the tagged affinity reagents include antibodies or antibody fragments.

6 . The method of claim 1 , wherein characterizing the plurality of proteins includes identifying post-translational modifications of the plurality of proteins.

7 . The method of claim 1 , wherein characterizing the plurality of proteins includes quantifying post-translational modifications of the plurality of proteins.

8 . The method of claim 1 , wherein the identity information includes individual probabilities of each protein of the plurality of proteins being each candidate protein of the set of candidate proteins.

9 . The method of claim 1 , wherein the tagged affinity reagents each have a binding affinity for a different epitope that is present in more than one of the proteins.

10 . A system for characterizing proteins in a sample comprising:

a substrate having a plurality of proteins from a sample, wherein individual proteins in the plurality of proteins are attached to unique spatial addresses on the substrate;

a detector configured to detect a series of affinity binding measurements associated with sequentially applying a series of tagged affinity reagents to the individual proteins in the plurality of proteins attached to the unique spatial addresses on the substrate and configured to produce an outcome set comprising positive binding outcomes and negative binding outcomes for the individual proteins in the plurality of proteins with the tagged affinity reagents; and

a computing system configured to:

obtain a database comprising a set of candidate proteins, and for each candidate protein, a probability of observing a positive binding outcome or negative binding outcome with each of the tagged affinity reagents;

characterize the plurality of proteins attached to the substrate by determining with a computer, using the database comprising the set of candidate proteins and the probabilities, and the outcome set, identity information for a probable group of candidate proteins in the database corresponding to each of the individual proteins attached to the substrate; and

store the characterization of each individual protein in the plurality of proteins and their corresponding unique spatial addresses on the substrate to a computer memory to characterize the individual proteins present in the sample.

11 . The system of claim 10 , wherein characterizing the plurality of proteins includes quantifying the candidate proteins in the plurality of proteins attached to the substrate.

12 . The system of claim 10 , wherein characterizing the plurality of proteins includes identifying the plurality of proteins attached to the substrate.

13 . The system of claim 12 , wherein the computing system is further configured to quantify the plurality of proteins based on the identification of the plurality of proteins attached to the substrate.

14 . The system of claim 10 , wherein the tagged affinity reagents include antibodies or antibody fragments.

15 . The system of claim 10 , wherein characterizing the plurality of proteins includes identifying post-translational modifications of the plurality of proteins.

16 . The system of claim 10 , wherein characterizing the plurality of proteins includes quantifying post-translational modifications of the plurality of proteins.

17 . A non-transitory computer-readable media having computer program instructions stored therein, the computer program instructions being configured such that, when executed by one or more computing devices, the computer program instructions cause the one or more computing devices to:

receive an outcome set indicating positive binding outcomes and negative binding outcomes taken from a process of sequentially applying a series of tagged affinity reagents to individual proteins in a plurality of proteins attached to unique spatial addresses on a substrate;

receive a database comprising a set of candidate proteins, and for each candidate protein, a probability of observing a positive binding outcome or negative binding outcome of the individual proteins with each of the tagged affinity reagents;

characterize the individual proteins of the plurality of proteins attached to the substrate by determining with a computer, using the database comprising the set of candidate proteins and the probabilities, and the outcome set, identity information for a probable group of candidate proteins in the database corresponding to each of the individual proteins attached to the substrate; and

store the characterization of the individual proteins of the plurality of proteins and their corresponding unique spatial addresses on the substrate to a computer memory to characterize the individual proteins present in the sample.

18 . The computer-readable media of claim 17 , wherein characterizing the plurality of proteins includes quantifying the candidate proteins in the plurality of proteins attached to the substrate.

19 . The computer-readable media of claim 17 , wherein characterizing the plurality of proteins includes identifying the plurality of proteins attached to the substrate.

20 . The computer-readable media of claim 19 , wherein the computer program instructions cause the one or more computing devices to quantify the plurality of proteins based on the identification of the plurality of proteins attached to the substrate.

21 . The computer-readable media of claim 17 , wherein the tagged affinity reagents include antibodies or antibody fragments.

22 . The computer-readable media of claim 17 , wherein characterizing the plurality of proteins includes identifying post-translational modifications of the plurality of proteins.

23 . The computer-readable media of claim 17 , wherein characterizing the plurality of proteins includes quantifying post-translational modifications of the plurality of proteins.

Assignments (2)

Continuity (6)

References Cited (289)