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

An automated system for sample preparation, the system comprising:

• (a) a fluid transfer unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system;
• (b) a sensor array comprising a magnetic support and a magnetic sensor array, wherein the magnetic sensor array comprises a plurality of partitions, wherein at least one of the plurality of partitions 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 silica and a carboxyl functionalized surface, wherein at least one of the plurality of magnetic particles is configured to bind to at least 300 different proteins from the biological sample, and wherein the magnetic support is configured to immobilize the plurality of magnetic particles when the magnetic sensor array is transferred to the magnetic support;
• (c) a reagent storage unit comprising supports for storing a plurality of reagents;
• (d) a waste unit comprising supports for storing a reagent to be disposed of;
• (e) a consumable storage unit comprising supports for storing a plurality of consumables for use by the multichannel fluid transfer instrument;
• and
• (f) a control unit comprising one or more processors programmed to perform steps comprising:
• (i) incubating the biological sample and the diluent with the plurality of magnetic particles in the at least one of the plurality of partitions of the magnetic sensor array such that proteins from the biological sample interact with at least one of the plurality of magnetic particles, wherein the incubating is performed using agitation and/or mixing at a temperature of 4° C. to 40° C. for at least 20 minutes;
• (ii) removing a supernatant from the at least one of the plurality of partitions of the magnetic sensor array to isolate the proteins interacting with at least one of the plurality of magnetic particles;
• (iii) washing the proteins interacting with at least one of the plurality of magnetic particles to obtain washed proteins interacting with the plurality of magnetic particles;
• and
• (iv) preparing a population of peptides for mass spectrometry, wherein the preparing comprises incubating a digestion solution with the washed proteins and at least one of the plurality of magnetic particles.