Granted Patent
B2
US 12,241,899 · App. 18/178,288 · Granted Mar 4, 2025
Systems and methods for sample preparation, data generation, and protein corona analysis
Inventors:
William Manning (Redwood City, CA); Young Kim (Union City, CA); Brandon Kwan-Leong (Daly City, CA); Hope Liou (Pleasanton, CA); Xiaoyan Zhao (Foster City, CA); Daniel Hornburg (Foster City, CA); Martin Goldberg (Saratoga, CA)
Assignee:
Seer, Inc.
G01N33/6848B01L3/5085B01L7/00G01N1/34G01N1/44G01N33/54326G01N33/54346B01L2400/043B82Y5/00B82Y25/00B82Y30/00B82Y35/00B82Y40/00
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Abstract
Systems and methods for automated sample preparation and processing of protein corona are described herein, as well as its application in the discovery of advanced diagnostic tools as well as therapeutic agents.
Claims (31)
1. An automated system for distinguishing states of a biological sample using a plurality of magnetic particles, the system comprising:
(a) a fluid transfer unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system, the multichannel fluid transfer instrument comprising a plurality of pipettes;
(b) a sensor array comprising a magnetic support and a magnetic sensor array, wherein the magnetic sensor array is removably coupled to the magnetic support and comprises a plurality of partitions that comprises (i) a biological sample, (ii) a diluent comprising a buffer, and (iii) a plurality of magnetic particles, wherein the plurality of magnetic particles comprise a carboxyl functionalized silica surface, and wherein the plurality of magnetic particles are configured to bind to at least 300 different proteins from the biological sample;
(c) a reagent storage unit comprising supports for storing a plurality of reagents, wherein the plurality of reagents comprise a buffer, a wash solution, a resuspension solution, and a denaturing solution comprising a protease, wherein the protease comprises trypsin;
(d) a waste unit comprising supports for storing a reagent to be disposed of;
(e) a consumable storage comprising supports for storing consumables for use by the multichannel fluid transfer instrument, the consumables comprising a plurality of pipette tips; and
(f) a control unit comprising one or more processors, wherein the one or more processors comprises a program to perform steps comprising:
i. contacting the biological sample with at least one partition of the plurality of partitions of the magnetic sensor array;
ii. incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array; and
iii. preparing a population of proteins for mass spectrometry by adding the resuspension solution and the denaturing solution to the partition to desorb and digest a plurality of proteins in the biological sample, thereby generating the population of proteins.
2. The automated system of claim 1 , wherein the biological sample are diluted with the diluent by about 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, or 8-fold.
3. The automated system of claim 1 , wherein the plurality of reagents comprises TE 150 mM KCL 0.05% CHAPS buffer.
4. The automated system of claim 1 , wherein the plurality of magnetic particles comprises a polydispersity index of 0.5 to 1.
5. The automated system of claim 1 , wherein the plurality of magnetic particles further comprise magnetic particles with a different physicochemical property chosen from the group consisting of surface charge, hydrophobicity, hydrophilicity, surface functionality, surface topography, surface curvature, porosity, core material, shell material, shape, size, composition and combinations thereof.
6. The automated system of claim 1 , wherein the magnetic support of the sensor array comprises a support for a multi-well plate.
7. The automated system of claim 6 , wherein the magnetic sensor array is a multi-well plate.
8. The automated system of claim 1 , wherein the sensor array comprises a thermal unit capable of maintaining a temperature while incubating the biological sample with the magnetic particles of the magnetic sensor array.
9. The automated system of claim 1 , wherein the sensor array comprises a rotational unit capable of physically agitating or mixing a sample.
10. The automated system of claim 1 , wherein the plurality of magnetic particles is are immobilized to the plurality of partitions.
11. The automated system of claim 1 , wherein the control unit is further programmed to transfer the magnetic sensor array to the magnetic support.
12. The automated system of claim 1 , wherein the biological sample comprises plasma or serum.
13. The automated system of claim 1 , wherein the (ii) incubating the biological sample with the plurality of magnetic particles contained within the at least one partition of the plurality of partitions of the magnetic sensor array comprises an incubation time of at least 25 minutes.
14. The automated system of claim 1 , wherein the (ii) incubating the biological sample with the plurality of magnetic particles contained within the at least one partition of the plurality of partitions of the magnetic sensor array comprises an incubation above room temperature.
15. The automated system of claim 1 , wherein the control unit is further programmed to perform a series of wash steps before (iii) desorbing and digesting the plurality of proteins in the biological sample.
16. The automated system of claim 1 , further comprising a consumable storage unit comprising supports for storing consumables for use by the multichannel fluid transfer instrument.
17. The automated system of claim 1 , further comprising:
(h) a mass spectrometer configured to receive the desorbed and digested plurality of proteins and to generate data comprising mass spectrometric or tandem mass spectrometric signals; and
(i) a computer comprising one or more computer processors and a computer readable medium comprising machine-executable code that, upon execution by the one or more computer processors, implements a method comprising:
i. generating a biomolecule fingerprint; and
ii. assigning a biological state based on the biomolecule fingerprint.
18. The automated system of claim 1 , wherein the automated system generates the desorbed and digested plurality of proteins in less than 7 hours.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Mar 28, 2024
From: MANNING, WILLIAM; KIM, YOUNG; KWAN-LEONG, BRANDON; LIOU, HOPE; ZHAO, XIAOYAN; HORNBURG, DANIEL; GOLDBERG, MARTIN
To: SEER, INC.
Reel/Frame 066940/0849 →
Continuity (4)
Continuation
PCTUS2020044908
· Aug 4, 2020
Provisional Application
62883107
· Aug 5, 2019
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