Proteomic Mapping

Where a protein works is often just as important as what it does. Proteins occupy different cellular compartments, assemble into complexes, and change their activity as cells respond to their surroundings. We develop chemical tools that label proteins in specific locations, helping us identify the molecular players at work inside living cells.

Our work began with enzyme-mediated proximity labeling. By targeting the engineered peroxidase APEX to a cellular compartment, we can tag nearby proteins and identify them by mass spectrometry without first isolating that compartment. This approach enabled proteomic mapping inside mitochondria, and improved chemical probes later extended APEX labeling to intact yeast cells (Science, 2013; Cell Chem. Biol., 2020).

Beyond identifying which proteins are present, we want to understand how local proteomes change over time. SubMAPP uses light or small molecules to activate proximity labeling, allowing us to track protein phosphorylation in specific compartments. With prox-SILAC, we combine proximity labeling with stable-isotope labeling to distinguish newly synthesized proteins from older ones. These tools reveal local changes in phosphorylation and protein turnover, including how the endoplasmic reticulum responds to cellular stress (PNAS, 2021; Nat. Commun., 2023).

Light gives us another way to control when labeling begins. Our photocatalytic labeling methods use genetically targeted proteins to trigger nearby chemical reactions. CAP-MS uses the blue-light-activated protein miniSOG to label local proteins, while the evolved photocatalyst Lantern enables labeling in less than a minute (Nat. Commun., 2023; Nat. Chem. Biol., 2026).

To move beyond blue light, we developed FLAPP, which pairs a genetically encoded fluorogen-activating protein with an iodinated malachite green dye. Binding to the protein turns on the dye’s fluorescence and enables near-infrared-driven labeling, helping keep background low. This red-shifted approach also allows light to penetrate deeper into tissue, extending the reach of spatial proteomic mapping (Anal. Chem., 2025).

How close must a protein be to receive a label? We are also investigating what sets the spatial reach of these reactions. Using DNA nanostructures to position targets at defined distances, we found that TurboID labeling was primarily contact-dependent in these assays. APEX2 also labeled efficiently within direct contact range, alongside a weaker contribution from diffusion to more distant phenols. These measurements help us understand what proximity-labeling maps capture and how to interpret them (Nat. Chem. Biol., 2025).