Spatial proteomics in neurons at single-protein resolution

Cell. 2024 Mar 28;187(7):1785-1800.e16. doi: 10.1016/j.cell.2024.02.045.


To understand biological processes, it is necessary to reveal the molecular heterogeneity of cells by gaining access to the location and interaction of all biomolecules. Significant advances were achieved by super-resolution microscopy, but such methods are still far from reaching the multiplexing capacity of proteomics. Here, we introduce secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a high-throughput imaging method that is capable of achieving virtually unlimited multiplexing at better than 15 nm resolution. Using SUM-PAINT, we generated 30-plex single-molecule resolved datasets in neurons and adapted omics-inspired analysis for data exploration. This allowed us to reveal the complexity of synaptic heterogeneity, leading to the discovery of a distinct synapse type. We not only provide a resource for researchers, but also an integrated acquisition and analysis workflow for comprehensive spatial proteomics at single-protein resolution.

Keywords: DNA-PAINT; excitatory synapses; inhibitory synapses; multiplexing; neuron atlas; neuron imaging; proteomics; spatial-omics; super-resolution microscopy; synapse; synapse diversity; synaptic proteins.

MeSH terms

  • DNA
  • Microscopy, Fluorescence / methods
  • Neurons
  • Proteins
  • Proteomics*
  • Single Molecule Imaging*


  • DNA
  • Proteins