2025/11/18 by Florian Bayer, Julian Müller, Nicole Kabella +9 · 1 voice
Chemistry · Biochemistry, Genetics and Molecular Biology · #Advanced Proteomics Techniques and Applications #Mass Spectrometry Techniques and Applications #Cell Image Analysis Techniques
paper · doi:10.1101/2025.11.18.689017
Abstract Mass-spectrometry-based phosphoproteomics enables the analysis of thousands of protein phosphorylation events across the human proteome. However, there is a lack of scalable, hypothesis-free, and statistically sound approaches for discovering, evaluating, and falsifying kinase::substrate relationships (KSRs). Here, we developed a new concept termed potency-coherence analysis. By measuring and integrating 17 million peptidoform-specific dose-response curves for 133 kinase inhibitors with known targets and affinities, we could critically re-evaluate published KSRs and discover thousands of potency-coherent and motif-plausible new KSRs for 96 human kinases. Application of these high-confidence KSRs enabled the estimation of kinase and signaling pathway activities in cancer patient biopsies. This unified and extendable framework has been implemented in ProteomicsDB to aid researchers in understanding the human phosphoproteome in health and disease.