Protein post-translational modifications (PTMs) tend to be dynamic and often occur at low stoichiometry, and thus can be challenging to identify and quantify. 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 poor response rates, poor overall survival statistics, and limited therapeutic options beyond chemotherapy. To identify potential therapeutic targets and therapeutic strategies for these tumors, we have applied functional proteomics with multiplexed isobaric tags (TMT) for quantification to gain insight into activated signaling networks. Application of this approach to triple negative breast cancer (TNBC) patient-derived xenograft tumors resulted in the identification of Src-family kinase signaling networks as potential targets for selected tumors. Extending these analyses to 150 human patient tumor specimens, we were able to identify activated networks in each patient tumor and to stratify patients into different categories based on their respective signaling networks and putative therapeutic targets. To enable reproducible quantification of low-abundance phosphorylation sites, in collaboration with ThermoFisher Scientific we developed SureQuant pTyr, a method enabling the targeted quantification of ~400 pTyr sites across almost all facets of cell biology. Using internal heavy-isotope labeled isotopologues for each tyrosine phosphorylated peptide of interest, SureQuant pTyr provides highly accurate and reproducible quantification that should be amenable to clinical proteomics.