Systems and methods for sample preparation, data generation, and protein corona analysis

1. An automated system for preparing a biological sample for mass spectrometry analysis using a plurality of magnetic particles comprising at least one physicochemical property, the system comprising:

(a) a fluid transfer unit comprising a multichannel fluid transfer instrument for transferring fluid between units within the system;

(b) a sample storage unit comprising a support for storing at least one biological sample;

(c) a sensing unit comprising a magnetic sensor array, wherein the magnetic sensor array comprises at least two partitions that comprise the plurality of magnetic particles, wherein the plurality of magnetic particles comprises physicochemical properties configured to bind a population of proteins comprising at least 300 protein groups within a biological sample, wherein the plurality of magnetic particles comprises a polydispersity index of at least 0.5, and wherein the support is configured to immobilize the plurality of magnetic particles when the magnetic sensor array is transferred to the support;

(d) a reagent storage unit comprising supports for storing a plurality of reagents;

(e) a waste unit comprising supports for storing a reagent to be disposed of;

(f) a magnetized support comprising a magnetic source; and

(g) a control unit comprising one or more processors programmed to perform steps comprising:

i. incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array under conditions sufficient to bind the population of proteins comprising at least 300 protein groups;

ii. applying the magnetized support to the magnetic sensor array to separate unbound sample from the plurality of magnetic particles;

iii. separating unbound components within the partition from the population of proteins and the plurality of magnetic particles; and

iv. preparing the population of proteins for mass spectrometry, wherein the preparing comprises incubating a digestion solution with the population of proteins and the plurality of magnetic particles.

2. The automated system of claim 1 , wherein the automated system further comprises a thermal unit capable of maintaining a temperature while incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array.

3. The automated system of claim 1 , wherein the automated system further comprises a rotational unit capable of physically agitating or mixing a sample.

4. The automated system of claim 1 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises incubating about 10 microliters to about 100 microliters of the biological sample with the plurality of magnetic particles.

5. The automated system of claim 4 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises incubating about 1 mg/mL to about 3 mg/mL of the plurality of magnetic particles.

6. The automated system of claim 1 , wherein the biological sample comprises plasma or serum.

7. The automated system of claim 1 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises an incubation time of at least 25 minutes.

8. The automated system of claim 7 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises an incubation above room temperature.

9. The automated system of claim 1 , wherein the control unit comprising one or more processors is further programmed to perform a series of wash steps before (iv) preparing the population of proteins for mass spectrometry.

10. The automated system of claim 1 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises incubating the biological sample with the plurality of magnetic particles and a diluent, wherein the diluent comprises a buffer, and wherein the biological sample is diluted at least 3-fold with the diluent.

11. The automated system of claim 1 , wherein the automated system generates the prepared population of proteins in less than 7 hours.

12. The automated system of claim 1 , wherein the plurality of magnetic particles comprises a silica surface.

13. The automated system of claim 1 , wherein the plurality of magnetic particles comprises a superparamagnetic iron oxide nanoparticle.

14. The automated system of claim 1 , wherein the plurality of magnetic particles comprises a negative surface charge.

15. An automated system for preparing a biological sample for mass spectrometry analysis using a plurality of magnetic particles comprising at least one physicochemical property, the system comprising:

(a) a fluid transfer unit comprising a multichannel fluid transfer instrument for transferring fluid between units within the system;

(b) a sample storage unit comprising a support for storing at least one biological sample;

(c) a sensing unit comprising a magnetic sensor array, wherein the magnetic sensor array comprises at least two partitions that comprise the plurality of magnetic particles wherein the plurality of magnetic particles comprises physicochemical properties configured to bind a population of proteins comprising at least 300 protein groups within a biological sample, wherein the plurality of magnetic particles comprises a poly(N-(3-(dimethylamino)propyl) methacrylamide) coating, and wherein the support is configured to immobilize the plurality of magnetic particles when the magnetic sensor array is transferred to the support;

(d) a reagent storage unit comprising supports for storing a plurality of reagents;

(e) a waste unit comprising supports for storing a reagent to be disposed of:

(f) a magnetized support comprising a magnetic source; and

(g) a control unit comprising one or more processors programmed to perform steps comprising:

i. incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array under conditions sufficient to bind the population of proteins comprising at least 300 protein groups;

ii. applying the magnetized support to the magnetic sensor array to separate unbound sample from the plurality of magnetic particles:

iii. separating unbound components within the at least two partitions from the population of proteins and the plurality of magnetic particles; and

iv. preparing the population of proteins for mass spectrometry, wherein the preparing comprises incubating a digestion solution with the population of proteins and the plurality of magnetic particles.

16. An automated system for preparing a biological sample for mass spectrometry analysis using a plurality of magnetic particles comprising at least one physicochemical property, the system comprising:

(a) a fluid transfer unit comprising a multichannel fluid transfer instrument for transferring fluid between units within the system;

(b) a sample storage unit comprising a support for storing at least one biological sample;

(c) a sensing unit comprising a magnetic sensor array, wherein the magnetic sensor array comprises at least two partitions that comprise the plurality of magnetic particles wherein the plurality of magnetic particles comprises physicochemical properties configured to bind a population of proteins comprising at least 300 protein groups within a biological sample, wherein the plurality of magnetic particles comprises a polydispersity index of 0.01 to 0.1, and wherein the support is configured to immobilize the plurality of magnetic particles when the magnetic sensor array is transferred to the support;

(d) a reagent storage unit comprising supports for storing a plurality of reagents;

(e) a waste unit comprising supports for storing a reagent to be disposed of:

(f) a magnetized support comprising a magnetic source; and

(g) a control unit comprising one or more processors programmed to perform steps comprising:

i. incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array under conditions sufficient to bind the population of proteins comprising at least 300 protein groups;

ii. applying the magnetized support to the magnetic sensor array to separate unbound sample from the plurality of magnetic particles:

iii. separating unbound components within the at least two partitions from the population of proteins and the plurality of magnetic particles; and iv. preparing the population of proteins for mass spectrometry, wherein the preparing comprises incubating a digestion solution with the population of proteins and the plurality of magnetic particles.

17. The automated system of claim 1 , wherein the plurality of magnetic particles is configured to bind the population of proteins that comprise from 300 to 2200 protein groups within the biological sample.

18. The automated system of claim 15 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises incubating about 10 microliters to about 100 microliters of the biological sample with the plurality of magnetic particles.

19. The automated system of claim 18 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises incubating about 1 mg/mL to about 3 mg/mL of the plurality of magnetic particles.

20. The automated system of claim 15 , wherein the biological sample comprises plasma or serum.

21. The automated system of claim 15 , wherein the plurality of magnetic particles comprises a superparamagnetic iron oxide nanoparticle.

22. The automated system of claim 15 , wherein the (i) incubating the biological sample with the plurality of magnetic particles of the magnetic sensor array comprises an incubation above room temperature.

23. The automated system of claim 15 , wherein the control unit comprising one or more processors is further programmed to perform a series of wash steps before (iv) preparing the population of proteins for mass spectrometry.

24. The automated system of claim 15 , wherein the plurality of magnetic particles is configured to bind the population of proteins that comprise from 300 to 2200 protein groups within the biological sample.

25. The automated system of claim 15 , wherein the automated system further comprises a thermal unit capable of maintaining a temperature while incubating the biological sample with the magnetic particles of the magnetic sensor array.

26. The automated system of claim 15 , wherein the automated system further comprises a rotational unit capable of physically agitating or mixing a sample.

27. The automated system of claim 1 , wherein the plurality of magnetic particles comprise microparticles.

28. The automated system of claim 10 , wherein the buffer comprises tris(hydroxymethyl)aminomethane (TRIS).

29. The automated system of claim 10 , wherein the biological sample is plasma or serum, and wherein the plurality of magnetic particles comprise microparticles with a negative surface charge.

30. The automated system of claim 15 , wherein the preparing the population of proteins for mass spectrometry comprises purifying the digested proteins using solid-phase extraction.