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. Author manuscript; available in PMC: 2025 Jun 20.
Published in final edited form as: Cell Chem Biol. 2024 May 20;31(6):1132–1144. doi: 10.1016/j.chembiol.2024.04.015

Table 2.

Examples of cell surface catalyst-based proximity labeling

Method Probe Targets Applications in Cell Surface Biology Notes Design
HRP

  1. Biotin-phenol

  2. Biotin-phenol

  3. Biotin-phenol

  4. Biotin-aniline

  5. Biotin-aniline

  1. Proteins

  2. Proteins

  3. Proteins

  4. RNAs

  5. RNAs

  1. Receptor tyrosine kinases clustering with B1 integrin

  2. Cell surface proteome of olfactory Projection Neurons (PNs) across development in Drosophila

  3. Cell surface proteins in close proximity to the Axon Initial Segment (AIS) cell adhesion molecule Neurofascin (Nfasc)

  4. Labeling of RNAs near complex N-glycans on cancer cell surfaces

  5. Labeling of RNAs near RNA binding proteins on cancer cell surfaces

  1. Cell surface probe combined with Aryl azide-biotin that was converted to an active radical by HRP 96.

  2. In vivo screen using transgenic HRP expresion, targeted to the cell Surface 75

  3. Primary antibodies against the extracellular domain of Nfasc used to direct HRP conjugated secondary antibodies to the AIS 97

  4. Lectin bound peroxidase labeling 2

  5. csRBP bound peroxidase labeling 12

 Probe:
> Available
Enzyme:
> Available
APEX/APEX2

  1. Biotin-phenol

  2. Biotin-phenol

  3. Biotin-phenol

  4. Biotin-phenol

  1. Proteins

  2. Proteins

  3. Proteins

  4. RNAs

  1. Substrates of Helicobacter pylori HtrA protease on the membrane of human stomach epithelial cells.

  2. Immediate consequences of calcium signaling on the extracellularly exposed proteome

  3. Proteomic mapping of mitochondrial and ER membranes

  4. Small RNAs in the ER lumen

  1. APEX2-fused HtrA enabled substrate labeling on the cell surface, Xie et al. 98

  2. Soluble purified APEX2 and biotin tyramide are used in SLAPSHOT as a general approach for monitoring extracellularly exposed protein dynamics, Tuomivaara et al. 99

  3. APEX2 genetically fused to ER and outer mitochondrial membrane protein for cytosol-facing labeling, Hung et al. 100

  4. Expression of HRP genetically fused to ER signal sequence with s6G incubation and biotin phenol labeling to specifically label ER lumen RNA species, Ren et al.15

 Probe:
> Available
Enzyme:
> Available
uMAP photocatalyst and dexter energy transfer Proteins Microenvironments on the cell surface, with shorter, more precise labeling strategies, e.g. PD-L1 Photocatalyst-antibody conjugate used to spatially localize carbene generation and selectively label protein-protein interactions on membranes, Geri et al.86 Probe:
> Available
Catalyst:
> Custom
MultiMap Eosin Y and diazirine biotin, aryl-azide-biotin, phenol-biotin Proteins Maps protein networks at various distances – short, intermediate and long range - from the photocatalyst, e.g. EGFR neighborhoods A single photocatalyst coupled with three photoprobes can generate three sets of protein network datasets at various distances from the POI, Lin et al.93 Probe:
> Available
Catalyst:
> Available