Comparative analysis of photocatalytic, enzymatic, and chemical approaches to identify canonical and noncanonical surfaceomes
5 affiliations
- 1Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- 2Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- 3Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
- 4Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
- 5Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
Abstract
The cell surface is a critical nexus in cellular communication and a rich landscape yielding the majority of current therapeutic targets, yet only a small fraction of cell surface proteins have been targeted therapeutically. The cell surface proteome (surfaceome) comprises only ~1% of the human proteome by mass, motivating enrichment strategies to detect surfaceome alterations in disease for drug target discovery. Developments in photocatalytic technology have revolutionized the study of protein neighborhoods around specific targets of interest, but photocatalysis has been underutilized for global surfaceome analysis. Here, we describe five distinct photocatalytic surfaceomics strategies, all without the need for cellular engineering, that apply the photocatalyst Eosin Y attached to different cell surface structures: direct glycan ligation, glycan attachment via two different lectins, membrane insertion, and free in extracellular space. We systematically compare these photocatalytic surfaceomics methods to each other as well as to three established chemical and enzymatic surfaceomics methods. We demonstrate that the different photocatalytic surfaceomics techniques achieve broadly similar canonical cell surface protein enrichment but show some important differences reflective of cell surface attachment mechanism. These mechanistically orthogonal surfaceomics techniques consistently identified numerous nonglycosylated proteins with high concordance, many of which represent an underappreciated class of noncanonical cell surface proteins lacking traditional cell surface protein features that may represent potential drug targets. This study substantially expands options for surfaceomics methods using photocatalytic proximity labeling.
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BibTeX
@article{ho2026comparative,
title = {{Comparative analysis of photocatalytic, enzymatic, and chemical approaches to identify canonical and noncanonical surfaceomes}},
author = {William W. Ho and Yifei Chen and Tomasz Slezak and Oleksandr Zginnyk and Trenton M. Peters-Clarke and Kaitlin Schaefer and Anthony A. Kossiakoff and Kevin K. Leung and James A. Wells},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = oct,
doi = {10.1073/pnas.2623700123},
url = {https://doi.org/10.1073/pnas.2623700123},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Comparative analysis of photocatalytic, enzymatic, and chemical approaches to identify canonical and noncanonical surfaceomes
AU - William W. Ho
AU - Yifei Chen
AU - Tomasz Slezak
AU - Oleksandr Zginnyk
AU - Trenton M. Peters-Clarke
AU - Kaitlin Schaefer
AU - Anthony A. Kossiakoff
AU - Kevin K. Leung
AU - James A. Wells
PY - 2026
DA - 2026/10/21
JO - Proceedings of the National Academy of Sciences of the United States of America
DO - 10.1073/pnas.2623700123
UR - https://doi.org/10.1073/pnas.2623700123
AB - The cell surface is a critical nexus in cellular communication and a rich landscape yielding the majority of current therapeutic targets, yet only a small fraction of cell surface proteins have been targeted therapeutically. The cell surface proteome (surfaceome) comprises only ~1% of the human proteome by mass, motivating enrichment strategies to detect surfaceome alterations in disease for drug target discovery. Developments in photocatalytic technology have revolutionized the study of protein neighborhoods around specific targets of interest, but photocatalysis has been underutilized for global surfaceome analysis. Here, we describe five distinct photocatalytic surfaceomics strategies, all without the need for cellular engineering, that apply the photocatalyst Eosin Y attached to different cell surface structures: direct glycan ligation, glycan attachment via two different lectins, membrane insertion, and free in extracellular space. We systematically compare these photocatalytic surfaceomics methods to each other as well as to three established chemical and enzymatic surfaceomics methods. We demonstrate that the different photocatalytic surfaceomics techniques achieve broadly similar canonical cell surface protein enrichment but show some important differences reflective of cell surface attachment mechanism. These mechanistically orthogonal surfaceomics techniques consistently identified numerous nonglycosylated proteins with high concordance, many of which represent an underappreciated class of noncanonical cell surface proteins lacking traditional cell surface protein features that may represent potential drug targets. This study substantially expands options for surfaceomics methods using photocatalytic proximity labeling.
SN - 0027-8424
SN - 1091-6490
ER -