Multiplexed proteomics and predictive drug candidate assessment

A computer program product tangibly embodying a set of instructions that, when executed by a processor, causes the processor to identify specific drug candidates for disease treatment by:

• for pairs of associated expressed proteins in a protein-protein interaction network for a plurality of biological samples, comparing relative concentration values of the associated proteins in each of the biological samples to identify outliers among a distribution of the relative concentration values;
• identifying a set of proteins involved in dysregulated protein-protein interactions in the network based on the outliers;
• and
• predicting an efficacy of one or more drug candidates from among a set of drug candidates for treating a disease based on the identified set of proteins and information about one or more of proteins, protein complexes, biological pathways, and functional modules targeted by the set of drug candidates.