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. Author manuscript; available in PMC: 2016 May 27.
Published in final edited form as: Nat Rev Drug Discov. 2015 Dec 16;15(3):204–216. doi: 10.1038/nrd.2015.16

Table 1. Characteristics and Capabilities of Single Cell Proteomics Methods.

Single Cell Proteomics Method Protein Detection Method Comments literature
Fluorescence Activated Cell Sorting (FACS) Staining with fluorophore-labeled antibodies

  • Standard for cell sorting based on membrane protein cell surface markers

  • High throughput tool with excellent statistics

  • Mature technique.

  • Multiplexing is colorimetric.

  • Typically requires large sample size;

  • Sorted and analyzed cells are viable and for subsequent analysis.

  • Commercial product (many vendors).

 References: 8, 11
Mass Cytometry (CyTOF) Staining fixed cells with mass-tag labeled antibodies

  • Good for cytoplasmic proteins;

  • Excellent statistics;

  • Demonstrated as a drug screening tool,

  • >30 proteins assayed per cell.

  • Multiplexing is via mass spectrometry.

  • Applicable to fixed tissue analysis.

  • Commercial product (Fluidigm). References

 References 13, 15, 39, 45, 108
Single Cell Barcode Chips (SCBCs) Spatially-encoded antibody array for fluorescent immuno-assays of secreted proteins or analytes released from lysed cells

  • Permits absolute quantitation.

  • Small (102-103 cells) biospecimen size ok.

  • Demonstration of >40 proteins assayed per cell.

  • Secreted proteins detected from viable cells.

  • Some designs integrate cell lysis to permit cytoplasmic protein assays and integrated protein/metabolite assays.

  • Analysis of cell-cell interactions.

  • Small (103-104 cells) biospecimen size ok.

  • Cost effective.

  • Multiplexing is via spatially encoded arrays.

  • Commercial Service (Isoplexis).

 References 12, 14, 27, 93, 95
MicroEngraving fluorescent immunoassays of secreted proteins

  • Small numbers of secreted proteins.

  • >104 single cells assayed in parallel.

  • Cost effective.

  • Permits kinetic studies of protein secretion

  • recovery of analyzed cells for further analysis

  • analysis of cell-cell interactions103.

  • Small (102-103 cells) biospecimen size ok.

  • Cost effective.

  • Multiplexing is colorimetric.

 References: 35, 80, 89, 103
Single Cell Western Blotting (scWestern) Miniaturized, automated Western Blotting on a microchip

  • Small (102-103 cells) biospecimen size ok.

  • 103 cells assayed per microchip

  • multiplexing to ∼12 proteins demonstrated

  • permits cytoplasmic proteins from lysed cells;

  • reasonably fast (4 hours).

  • Provides protein ladder reference.

  • Relative quantitation.

 References 81