Depletion of hemoglobin and carbonic anhydrase from erythrocyte cytosolic samples by preparative clear native electrophoresis

Nat Protoc. 2011 Dec 8;7(1):36-44. doi: 10.1038/nprot.2011.427.


Proteomic analysis of red cells is compromised by the presence of high-abundance proteins (hemoglobin and carbonic anhydrase-1), which completely obscure low-abundance species. The depletion method presented here involves performing native gel electrophoresis in a polyacrylamide gel tube using a modified electroelution cell. The electrophoretic run is interrupted intermittently to allow the recovery of at least three different liquid fractions, which can be analyzed by both native PAGE and 2D isoelectric focusing SDS-PAGE, or by shotgun mass spectrometry analysis after trypsin in-solution protein digestion. This low-cost, reproducible technique can be used to process large amounts of sample, and it increases the likelihood of detecting low-abundance proteins, thereby resulting in greater proteome coverage. The separation procedure takes approximately 6-7 h.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbonic Anhydrases / chemistry
  • Cytosol / chemistry
  • Electrophoresis, Polyacrylamide Gel / methods*
  • Erythrocytes / chemistry*
  • Hemoglobins / chemistry
  • Isoelectric Focusing
  • Mass Spectrometry
  • Proteomics / methods*


  • Hemoglobins
  • Carbonic Anhydrases