Peters-Clarke, T. | Search bioRxiv

bioRxiv2026

High-resolution photocatalytic crosslinking of protein neighborhoods using contact-dependent antibody mapping (contactMAP)

Photo-proximity labeling proteomics (PLP) has emerged as a powerful method for rapid and temporal mapping of transient and fragile protein-protein interactions, especially those in membranes. Numerous catalysts can trigger highly reactive diffusive biotinylated probes to label protein neighborhoods at various length scales. Photocatalysts can also trigger protein crosslinking, predominantly between neighboring tyrosines or between histidine and lysine residues. We have exploited this sidechain directed crosslinking for photo-PLP, in a method we call contactMAP. Using biotinylated antibody binders to photocrosslink Her2 or EGFR neighborhoods, contactMAP enriched high resolution maps of these cancer-associated protein neighborhoods in a manner that rivals or outperforms established photo-PLP methods. ContactMAP is an extraordinarily simple and democratic photo-PLP labeling method with broad applications for probing biomolecular interactions in complex mixtures.

Cancer Biology↗

bioRxiv2024

Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Activated Ion-Tandem Mass Tags (AI-TMT)

Single-cell proteomics is a powerful approach to precisely profile protein landscapes within individual cells toward a comprehensive understanding of proteomic functions and tissue and cellular states. The inherent challenges associated with limited starting material in single-cell analyses demands heightened analytical sensitivity. Just as advances in sample preparation maximize the amount of material that makes it from the cell to the mass spectrometer, we strive to maximize the number of ions that make it from ion source to the detector. In isobaric tagging experiments, limited reporter ion generation limits quantitative accuracy and precision. The combination of infrared photoactivation and ion parking circumvents the m/z dependence inherent in HCD, maximizing reporter generation and avoiding unintended degradation of TMT reporter molecules in a method we term activated ion-tandem mass tags (AI-TMT). The method was applied to single-cell human proteomes using 18-plex TMTpro, resulting in a 4-5-fold increase in reporter ion signal on average compared to conventional SPS-MS3 approaches. AI-TMT enables faster duty cycles, higher throughput, and increased peptide identification and quantification. Comparative experiments showcase 4-5-fold lower injection times for AI-TMT, providing superior sensitivity without compromising accuracy. In all, AI-TMT enhances the sensitivity and dynamic range of proteomic experiments and is compatible with other techniques, including gas-phase fractionation and real-time searching, promising increased gains in the study of cellular heterogeneity and disease mechanisms.

biochemistry↗