Protein post-translational modifications (PTMs) regulate many aspects of protein function, including localization, activation, stability, and protein-protein interactions. Protein PTMs tend to be dynamic and often occur at low stoichiometry, and thus can be challenging to identify and quantify. Indeed, enrichment of the selected PTM, or even subsets of the selected PTM, are often required prior to analysis. Despite these inherent challenges, PTM analyses (e.g., functional proteomics) can provide unprecedented insight into biological regulation in the context of health and disease, including identification of therapeutic drug targets, mechanisms of therapeutic resistance, and response to environmental perturbagens. Many cancer subtypes have limited therapeutic options beyond chemotherapy, and poor response rates and overall survival statistics. To identify potential therapeutic targets and therapeutic strategies, we have applied functional proteomics with multiplexed isobaric tags (TMT) for quantification to gain insight into activated signaling networks. Application of this approach to chemotherapy resistant triple negative breast cancer (CR-TNBC) identified a therapeutic target and biomarker signature. Modification of our functional proteomics approach has enabled multiplexed quantification of hundreds of signaling nodes in single sections or punches of FFPE-preserved tumor tissues, enabling the potential for a proteomics-based approach to personalized medicine.