# US 12,222,349 B2 · Compositions, methods and systems for protein corona analysis and uses thereof

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- Number: US 12,222,349 B2
- Document ID: US12222349B2
- Status: Granted
- Kind: B2
- Application number: 17/216,514
- Filed: 2021-03-29
- Published: 2021-07-15
- Granted: 2025-02-11
- Earliest claimed: 2018-11-07
- Assignees: Seer, Inc.
- Applicants: Seer, Inc.
- Inventors: Hongwei Xia; Lyndal Hesterberg; Michael Figa; Xiaoyan Zhao; Gregory Troiano; William Manning; John Blume; Omid Farokhzad; Matthew McLean; Craig Stolarczyk; Marwin Ko; Theodore Platt
- Web page: https://patentgrep.com/patent/US12222349B2

## CPC

- G01N 33/54326: {Magnetic particles}
- G01N 33/54346: {Nanoparticles}
- G01N 33/551: the carrier being inorganic
- G01N 33/6848: {Methods of protein analysis involving mass spectrometry}
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

Compositions, methods, and systems for analyzing the protein corona are described herein, as well as its application in the discovery of advanced diagnostic tools as well as therapeutic targets.

## Claims

### Claim 1

A kit for identifying proteins in a biological sample, comprising:
(a) a plurality of magnetic particles configured to bind a plurality of proteins in the biological sample when the plurality of magnetic particles is incubated with the biological sample, wherein the plurality of magnetic particles comprise a polymer, wherein the polymer comprises an ammonium functional group, wherein the polymer comprises a recurring unit of:
wherein the plurality of magnetic particles comprise a positive zeta potential, and wherein the positive zeta potential of the plurality of magnetic particles range from 10 mV to 60 mV;
(b) a reducing agent configured to reduce the plurality of proteins; and
(c) an enzymatic agent configured to digest the plurality of proteins.

### Claim 2 (depends on 1)

The kit of claim 1, wherein the polymer comprises poly(N-(3-(dimethylamino)propyl)methacrylamide) (PDMAPMA).

### Claim 3 (depends on 2)

The kit of claim 2, wherein the plurality of magnetic particles comprises iron oxide.

### Claim 4 (depends on 3)

The kit of claim 3, wherein the plurality of magnetic particles comprise a plurality of nanoparticles.

### Claim 5 (depends on 4)

The kit of claim 4, wherein a polydispersity index of the plurality of magnetic particles is less than 0.5.

### Claim 6 (depends on 1)

The kit of claim 1, further comprising an alkylating agent for alkylating the plurality of proteins.

### Claim 7 (depends on 6)

The kit of claim 6, further comprising an elution buffer for eluting digested proteins.

### Claim 8 (depends on 1)

The kit of claim 1, wherein the plurality of magnetic particles is configured to bind at least 200 unique proteins when incubated with the biological sample.

### Claim 9 (depends on 1)

The kit of claim 1, wherein the positive zeta potential of the plurality of magnetic particles range from 20 mV to 40 mV.

### Claim 10 (depends on 1)

The kit of claim 1, further comprising (d) a solid-phase for purifying a plurality of peptides using solid-phase extraction.

### Claim 11

A kit for identifying proteins in a biological sample, comprising:
(a) a plurality of magnetic particles configured to bind a plurality of proteins in the biological sample when the plurality of magnetic particles is incubated with the biological sample, wherein the plurality of magnetic particles comprise a polymer, wherein the polymer comprises an ammonium functional group, wherein the ammonium functional group comprises a tertiary ammonium, wherein the plurality of magnetic particles comprise a positive zeta potential, and wherein the positive zeta potential of the plurality of magnetic particles range from 10 mV to 60 mV;
(b) a reducing agent configured to reduce the plurality of proteins; and
(c) an enzymatic agent configured to digest the plurality of proteins.

### Claim 12

A kit for identifying proteins in a biological sample, comprising:
(a) a plurality of magnetic particles configured to bind a plurality of proteins in the biological sample when the plurality of magnetic particles is incubated with the biological sample, wherein the plurality of magnetic particles comprise a polymer, wherein the polymer comprises an ammonium functional group, wherein the ammonium functional group comprises a quaternary ammonium, wherein the plurality of magnetic particles comprise a positive zeta potential, and wherein the positive zeta potential of the plurality of magnetic particles range from 10 mV to 60 mV;
(b) a reducing agent configured to reduce the plurality of proteins; and
(c) an enzymatic agent configured to digest the plurality of proteins.

### Claim 13 (depends on 1)

The kit of claim 1, wherein the plurality of magnetic particles comprises a plurality of microparticles.

### Claim 14 (depends on 1)

The kit of claim 1, wherein the polymer is cross-linked.

### Claim 15

A kit for identifying proteins in a biological sample, comprising:
(a) a plurality of magnetic particles configured to bind a plurality of proteins in the biological sample when the plurality of magnetic particles is incubated with the biological sample, wherein the plurality of magnetic particles comprise a polymer, wherein the polymer comprises divinylbenzene, and wherein the plurality of magnetic particles comprise a positive zeta potential;
(b) a reducing agent configured to reduce the plurality of proteins; and
(c) an enzymatic agent configured to digest the plurality of proteins.

### Claim 16 (depends on 1)

The kit of claim 1, further comprising (d) a buffer configured to maintain acidic pH conditions when the plurality of magnetic particles is incubated with the biological sample.

### Claim 17 (depends on 8)

The kit of claim 8, wherein the plurality of magnetic particles is configured to bind to at least 400 unique proteins when incubated with the biological sample.

### Claim 18 (depends on 1)

The kit of claim 1, wherein the plurality of magnetic particles are porous.

### Claim 19 (depends on 11)

The kit of claim 11, wherein the plurality of magnetic particles comprises iron oxide.

### Claim 20 (depends on 19)

The kit of claim 19, wherein the plurality of magnetic particles comprise a plurality of nanoparticles.

### Claim 21 (depends on 11)

The kit of claim 11, wherein the plurality of magnetic particles is configured to bind at least 200 unique proteins when incubated with the biological sample.

### Claim 22 (depends on 11)

The kit of claim 11, further comprising (d) a solid-phase for purifying a plurality of peptides using solid-phase extraction.

### Claim 23 (depends on 11)

The kit of claim 11, wherein the plurality of magnetic particles comprises a plurality of microparticles.

### Claim 24 (depends on 11)

The kit of claim 11, wherein the polymer is cross-linked.

### Claim 25 (depends on 12)

The kit of claim 12, wherein the plurality of magnetic particles comprises iron oxide.

### Claim 26 (depends on 25)

The kit of claim 25, wherein the plurality of magnetic particles comprise a plurality of nanoparticles.

### Claim 27 (depends on 12)

The kit of claim 12, wherein the plurality of magnetic particles is configured to bind at least 200 unique proteins when incubated with the biological sample.

### Claim 28 (depends on 12)

The kit of claim 12, further comprising (d) a solid-phase for purifying a plurality of peptides using solid-phase extraction.

### Claim 29 (depends on 12)

The kit of claim 12, wherein the plurality of magnetic particles comprises a plurality of microparticles.

### Claim 30 (depends on 12)

The kit of claim 12, wherein the polymer is cross-linked.

### Claim 31 (depends on 15)

The kit of claim 15, wherein the plurality of magnetic particles comprises iron oxide.

### Claim 32 (depends on 31)

The kit of claim 31, wherein the plurality of magnetic particles comprise a plurality of nanoparticles.

### Claim 33 (depends on 15)

The kit of claim 15, wherein the plurality of magnetic particles is configured to bind at least 200 unique proteins when incubated with the biological sample.

### Claim 34 (depends on 15)

The kit of claim 15, further comprising (d) a solid-phase for purifying a plurality of peptides using solid-phase extraction.

### Claim 35 (depends on 15)

The kit of claim 15, wherein the plurality of magnetic particles comprises a plurality of microparticles.

### Claim 36 (depends on 15)

The kit of claim 15, wherein the polymer is cross-linked.