Comprehensive measurement of respiratory activity in permeabilized cells using extracellular flux analysis

Nat Protoc. 2014 Feb;9(2):421-38. doi: 10.1038/nprot.2014.018. Epub 2014 Jan 23.


Extracellular flux (XF) analysis has become a mainstream method for measuring mitochondrial function in cells and tissues. Although this technique is commonly used to measure bioenergetics in intact cells, we outline here a detailed XF protocol for measuring respiration in permeabilized cells. Cells are permeabilized using saponin (SAP), digitonin (DIG) or recombinant perfringolysin O (rPFO) (XF-plasma membrane permeabilizer (PMP) reagent), and they are provided with specific substrates to measure complex I- or complex II-mediated respiratory activity, complex III+IV respiratory activity or complex IV activity. Medium- and long-chain acylcarnitines or glutamine may also be provided for measuring fatty acid (FA) oxidation or glutamine oxidation, respectively. This protocol uses a minimal number of cells compared with other protocols and does not require isolation of mitochondria. The results are highly reproducible, and mitochondria remain well coupled. Collectively, this protocol provides comprehensive and detailed information regarding mitochondrial activity and efficiency, and, after preparative steps, it takes 6-8 h to complete.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Bacterial Toxins / metabolism
  • Cell Line
  • Cell Respiration / physiology*
  • Digitonin / metabolism
  • Electron Transport Chain Complex Proteins / metabolism
  • Hemolysin Proteins / metabolism
  • Metabolic Flux Analysis / methods*
  • Mitochondria / physiology*
  • Oxygen Consumption / physiology
  • Rats
  • Saponins / metabolism


  • Bacterial Toxins
  • Electron Transport Chain Complex Proteins
  • Hemolysin Proteins
  • Saponins
  • Clostridium perfringens theta-toxin
  • Digitonin