Proteomic approaches for interrogating kinase signaling networks

Kinases are central regulators of multiple signaling cascades, controlling processes such as cellular growth, proliferation, and differentiation. Given their vital role within the cell, dysregulated kinase activity contributes to several skin diseases, including melanoma and dermatitis. Poor disease response or resistance to targeted inhibitors can be driven by adaptive kinase responses. Genomic assays are highly informative but do not accurately capture kinase abundance and activity at the protein level. In this paper, we review 2 complementary mass spectrometry-based proteomics methods for functional kinome analysis that are readily applicable to dermatology research. Multiplexed inhibitor beads coupled with mass spectrometry (MIB-MS) uses broad-spectrum, immobilized kinase inhibitors to enrich for kinases in active conformation, providing an unbiased, pathway-level readout of kinase network dynamics, adaptive rewiring, and drug specificity. Internal standard triggered-parallel reaction monitoring (IS-PRM)-targeted proteomics, including the Thermo SureQuant acquisition method, leverages heavy peptide triggers to deliver sensitive, consistent quantification of predefined kinase peptides from limited input clinical specimens, including formalin fixed, paraffin embedded. We summarize optimized workflows, instrument set-up, sample requirements, technical considerations, and limitations. Together, MIB-MS and IS-PRM SureQuant offer orthogonal, scalable strategies to profile kinase networks in skin biology and to inform target discovery, biomarker development, and rational therapeutic strategies.