Systems and Methods for Targeted Therapy Based on Single-Cell Stimulus Perturbation Response

A method for optimizing stimulus combinations for therapy, the method comprising:

• receiving a cell sample;
• treating the cell sample with a plurality of stimuli by treating a different portion of the cell sample with one of the plurality of stimuli for each of the plurality of stimuli;
• labeling the treated cell sample with a plurality of metal-conjugated antibodies, wherein the plurality of metal-conjugated antibodies corresponds with a set of markers;
• analyzing the labeled cell sample using a mass spectrometer;
• obtaining mass spectrometry data from the mass spectrometer, wherein the mass spectrometry data describe perturbation responses;
• identifying subpopulations within the cell sample using the mass spectrometry data using a computing device;
• computing stimulus effects using the mass spectrometry data using the computing device;
• generating a nested-effects model using the mass spectrometry data and the stimulus effects using the computing device, wherein the nested-effects model describes the relationships between the plurality of stimuli and the set of markers across the subpopulations;
• scoring stimulus combinations using the nested-effects model using the computing device, wherein the stimulus combinations are combinations made from the plurality of stimuli;
• and
• outputting a list of ranked stimulus combinations based on the scored stimulus combinations.