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

Nature Protocols

Volumn 7, Issue 1, 2012, Pages 36-44

  D'Amici, Gian Maria ^a   Rinalducci, Sara ^a   Zolla, Lello ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONATE DEHYDRATASE; HEMOGLOBIN; POLYACRYLAMIDE GEL; REAGENT; TRYPSIN;

ARTICLE; CLINICAL PROTOCOL; CONCENTRATION (PARAMETERS); COST MINIMIZATION ANALYSIS; CYTOSOL; ELUTION; ERYTHROCYTE; EXPERIMENTAL DESIGN; FREEZING; GEL ELECTROPHORESIS; MASS SPECTROMETRY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN DEPLETION; PROTEIN DETERMINATION; PROTEIN ISOLATION; PROTEOMICS; SEPARATION TECHNIQUE;

CARBONIC ANHYDRASES; CYTOSOL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ERYTHROCYTES; HEMOGLOBINS; ISOELECTRIC FOCUSING; MASS SPECTROMETRY; PROTEOMICS;

EID: 83455178273     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2011.427     Document Type: Article

References (40)

1. Misra, H.P. & Fridovich, I. The generation of superoxide radical during the autoxidation of hemoglobin. J. Biol. Chem. 247, 6960-6962 (1972).
2. Kriebardis, A.G. et al. Progressive oxidation of cytoskeletal proteins and accumulation of denatured hemoglobin in stored red cells. J. Cell. Mol. Med. 11, 148-155 (2007). (Pubitemid 46439633)
3. van Wijk, R. & van Solinge, W.W. The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis. Blood 106, 4034-4042 (2005). (Pubitemid 41775906)
4. An, X. & Mohandas, N. Disorders of red cell membrane. Br. J. Haematol. 141, 367-375 (2008). (Pubitemid 351521152)
5. Low, T.Y., Seow, T.K. & Chung, M.C. Separation of human erythrocyte membrane associated proteins with one-dimensional and two-dimensional gel electrophoresis followed by identifcation with matrix-assisted laser desorption/ionization-time of fight mass spectrometry. Proteomics 2, 1229-1239 (2002).
6. Kakhniashvili, D.G., Bulla, L.A. & Goodman, S.R. The human erythrocyte proteome: analysis by ion trap tandem mass spectrometry. Mol. Cell. Proteomics. 3, 501-509 (2004). (Pubitemid 38714291)
7. Tyan, Y.C. et al. Proteomic profling of erythrocyte proteins by proteolytic digestion chip and identifcation using two-dimensional electrospray ionization tandem mass spectrometry. J. Proteome Res. 4, 748-757 (2005).
8. Pasini, E.M. et al. In-depth analysis of the membrane and cytosolic proteome of red blood cells. Blood 108, 791-801 (2006). (Pubitemid 44154609)
9. Bhattacharya, D., Mukhopadhyay, D. & Chakrabarti, A. Hemoglobin depletion from red blood cell cytosol reveals new proteins in 2-D gel-based proteomics study. Proteomics Clin. Appl. 1, 561-564 (2007).
10. Alvarez-Llamas, G. et al. A novel methodology for the analysis of membrane and cytosolic sub-proteomes of erythrocytes by 2-DE. Electrophoresis 30, 4095-4108 (2009).
11. Ringrose, J.H. et al. Highly effcient depletion strategy for the two most abundant erythrocyte soluble proteins improves proteome coverage dramatically. J. Proteome Res. 7, 3060-3063 (2008).
12. Roux-Dalvai, F. et al. Extensive analysis of the cytoplasmic proteome of human erythrocytes using the peptide ligand library technology and advanced mass spectrometry. Mol. Cell. Proteomics 7, 2254-2269 (2008).
13. Pasini, E.M., Lutz, H.U., Mann, M. & Thomas, A.W. Red blood cell (RBC) membrane proteomics-Part I: proteomics and RBC physiology. J. Proteomics 73, 403-420 (2010).
14. Pasini, E.M., Lutz, H.U., Mann, M. & Thomas, A.W. Red blood cell (RBC) membrane proteomics-Part II: comparative proteomics and RBC patho-physiology. J. Proteomics 73, 421-435 (2010).
15. Echan, L.A., Tang, H.Y., Ali-Khan, N., Lee, K. & Speicher, D.W. Depletion of multiple high-abundance proteins improves protein profling capacities of human serum and plasma. Proteomics 5, 3292-3303 (2005). (Pubitemid 41192036)
16. Liu, T. et al. Evaluation of multiprotein immunoaffnity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol. Cell. Proteomics 5, 2167-2174 (2006). (Pubitemid 44817028)
17. Thulasiraman, V. et al. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis 26, 3561-3571 (2005). (Pubitemid 41410379)
18. Guerrier, L. et al. Reducing protein concentration range of biological samples using solid-phase ligand libraries. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 833, 33-40 (2006).
19. Greening, D.W. & Simpson, R.J. A centrifugal ultrafltration strategy for isolating the low-molecular weight (< or=25K) component of human plasma proteome. J. Proteomics 73, 637-648 (2010).
20. Lee, H.J., Lee, E.Y., Kwon, M.S. & Paik, Y.K. Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics. Curr. Opin. Chem. Biol. 10, 42-49 (2006).
21. Ichibangase, T., Moriya, K., Koike, K. & Imai, K. Limitation of immunoaffnity column for the removal of abundant proteins from plasma in quantitative plasma proteomics. Biomed. Chromatogr. 23, 480-487 (2009).
22. Righetti, P.G. & Boschetti, E. The ProteoMiner and the FortyNiners: searching for gold nuggets in the proteomic arena. Mass. Spectrom. Rev. 27, 596-608 (2008).
23. Guerrier, L., Righetti, P.G. & Boschetti, E. Reduction of dynamic protein concentration range of biological extracts for the discovery of low-abundance proteins by means of hexapeptide ligand library. Nat. Protoc. 3, 883-890 (2008). (Pubitemid 351639032)
24. Sennels, L. et al. Proteomic analysis of human blood serum using peptide library beads. J. Proteome Res. 6, 4055-4062 (2007). (Pubitemid 350032568)
25. Castagna, A. et al. Exploring the hidden human urinary proteome via ligand library beads. J. Proteome Res. 4, 1917-1930 (2005). (Pubitemid 41814257)
26. Guerrier, L. et al. Exploring the platelet proteome via combinatorial, hexapeptide ligand libraries. J. Proteome Res. 6, 4290-4303 (2007). (Pubitemid 350158505)
27. D'Amato, A. et al. In-depth exploration of cow's whey proteome via combinatorial peptide ligand libraries. J. Proteome Res. 8, 3925-3936 (2009).
28. Fasoli, E. et al. Popeye strikes again: the deep proteome of spinach leaves. J. Proteomics 74, 127-136 (2011).
29. Bandow, J.E. Comparison of protein enrichment strategies for proteome analysis of plasma. Proteomics 10, 1416-1425 (2010).
30. Boschetti, E. & Righetti, P.G. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 9, 1492-1510 (2009).
31. Boschetti, E., Bindschedler, L.V., Tang, C., Fasoli, E. & Righetti, P.G. Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price. J. Chromatogr. A 1216, 1215-1222 (2008).
32. Keidel, E.M., Ribitsch, D. & Lottspeich, F. Equalizer technology-equal rights for disparate beads. Proteomics 10, 2089-2098 (2010).
33. Fasoli, E. et al. Interaction among proteins and peptide libraries in proteome analysis: pH involvement for a larger capture of species. J. Proteomics 73, 733-742 (2010).
34. Prabakaran, S. et al. 2-D DIGE analysis of liver and red blood cells provides further evidence for oxidative stress in schizophrenia. J. Proteome Res. 6, 141-149 (2007). (Pubitemid 46173666)
35. Levine, J. et al. Identifcation of a nickel(II) binding site on hemoglobin which confers susceptibility to oxidative deamination and intramolecular cross-linking. J. Biol. Chem. 273, 13037-13046 (1998). (Pubitemid 28246868)
36. D'Amici, G.M., Rinalducci, S. & Zolla, L. An easy preparative gel electrophoretic method for targeted depletion of haemoglobin in erythrocyte cytosolic samples. Electrophoresis 32, 1319-1322 (2011).
37. Wittig, I., Braun, H.P. & Schägger, H. Blue native PAGE. Nat. Protoc. 1, 418-428 (2006).
38. Wittig, I., Karas, M. & Schägger, H. High-resolution clear native electrophoresis for in-gel functional assays and fuorescence studies of membrane protein complexes. Mol. Cell. Proteomics 6, 1215-1225 (2007). (Pubitemid 47099231)
39. Gerton, G.L., Wardrip, N.J. & Hedrick, J.L. A gel eluter for recovery of proteins separated by polyacrylamide gel electrophoresis. Anal. Biochem. 126, 116-121 (1982).
40. Bradford, M.M. A rapid and sensitive for method the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254 (1976).