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How to Bring the “Unseen” Proteome to the Limelight via Electrophoretic Pre-Fractionation Techniques

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Bioscience Reports

Abstract

The present review reports a panoply of electrophoretic methods as pre-fractionation tools in proteomic investigations in preparation for mass spectrometry or two-dimensional electrophoresis map analysis. Such electrophoretic pre-fractionation protocols include all those electrokinetic methodologies which are performed in free solution, most of them relying on isoelectric focusing steps (although some approaches based on gels and granulated media are also discussed). Devices associated with electrophoretic separations are multi-chamber apparatuses, such as the multi-compartment electrolyzers equipped with either isoelectric membranes or with isoelectric beads, Off-Gel electrophoresis in a multi-cup device and the Rotofor, an instrument also based on a multi-chamber system but exploiting the conventional technique of carrier-ampholyte-focusing. Other free-flow systems, as well as miniaturized chambers, are also described.

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Abbreviations

FFE:

free-flow electrophoresis

FF-IEF:

free-flow isoelectric focusing

IPG:

immobilized pH gradients

CBI:

codon bias index

EOF:

electroendoosmotic flow

2-DE:

two-dimensional electrophoresis

References

  • L. N. Anderson N. G. Anderson (2002) Mol. Cell. Proteomics 1 845–867 Occurrence Handle10.1074/mcp.R200007-MCP200 Occurrence Handle12488461

    Article  PubMed  Google Scholar 

  • I. L. Arnaud J. Josserand J. S. Rossier H. H. Girault (2002) Electrophoresis 23 3253–3261 Occurrence Handle10.1002/1522-2683(200210)23:19<3253::AID-ELPS3253>3.0.CO;2-4 Occurrence Handle12373750

    Article  PubMed  Google Scholar 

  • S. H. Bae A. G. Harris P. G. Hains H. Chen D. E. Garfin S. L. Hazell Y. K. Paik B. Walsh S. J. Cordwell (2003) Proteomics 3 569–579 Occurrence Handle10.1002/pmic.200300392 Occurrence Handle12748937

    Article  PubMed  Google Scholar 

  • M. Bier (1998) Electrophoresis 19 1057–1063 Occurrence Handle10.1002/elps.1150190703 Occurrence Handle9662165

    Article  PubMed  Google Scholar 

  • Bier, M., Mosher, R. A., Thormann, W., and Graham, A. (1984) In: Electrophoresis ’83 (H. Hirai, ed.), de␣Gruyter, Berlin, pp. 99–107.

  • E. Bordini M. Hamdan P. G. Righetti (2000) Rapid Commun. Mass Spectrom. 14 840–848 Occurrence Handle10.1002/(SICI)1097-0231(20000530)14:10<840::AID-RCM953>3.0.CO;2-M Occurrence Handle10825247

    Article  PubMed  Google Scholar 

  • D. Burggraf G. Weber F. Lottspeich (1995) Electrophoresis 16 1010–1015 Occurrence Handle10.1002/elps.11501601169 Occurrence Handle7498121

    Article  PubMed  Google Scholar 

  • N. Campostrini L.B. Areces J. Rappsilber M.C. Pietrogrande F. Dondi F. Pastorino M. Ponzoni P.G. Righetti (2005) Proteomics 5 2385–2395 Occurrence Handle10.1002/pmic.200401253 Occurrence Handle15880804

    Article  PubMed  Google Scholar 

  • M. Chiari P. G. Righetti A. Negri F. Ceciliani S. Ronchi (1992) Electrophoresis 13 882–884 Occurrence Handle10.1002/elps.11501301193 Occurrence Handle1483433

    Article  PubMed  Google Scholar 

  • S. J. Cordwell A. S. Nouwens N. M. Verrills D. J. Basseal B. J. Walsh (2000) Electrophoresis 21 1094–1103 Occurrence Handle10.1002/(SICI)1522-2683(20000401)21:6<1094::AID-ELPS1094>3.0.CO;2-0 Occurrence Handle10786883

    Article  PubMed  Google Scholar 

  • G. L. Corthals M. P. Molloy B. R. Herbert K. L. Williams A. A. Gooley (1997) Electrophoresis 18 317–323 Occurrence Handle10.1002/elps.1150180304 Occurrence Handle9150908

    Article  PubMed  Google Scholar 

  • G. L. Corthals C. V. Wasinger D. F. Hochstrasser J. C. Sanchez (2000) Electrophoresis 21 1104–1115 Occurrence Handle10.1002/(SICI)1522-2683(20000401)21:6<1104::AID-ELPS1104>3.0.CO;2-C Occurrence Handle10786884

    Article  PubMed  Google Scholar 

  • K. Cottingham (2003) J. Proteome Res. 2 574–574

    Google Scholar 

  • M. Cretich G. Pirri G. Carrea M. Chiari (2003) Electrophoresis 24 577–581 Occurrence Handle10.1002/elps.200390067 Occurrence Handle12601724

    Article  PubMed  Google Scholar 

  • P. Davidsson L. Paulson C. Hesse K. Blennow C. L. Nilsson (2001) Proteomics 1 444–452 Occurrence Handle10.1002/1615-9861(200103)1:3<444::AID-PROT444>3.3.CO;2-H Occurrence Handle11680889

    Article  PubMed  Google Scholar 

  • M. Dreger (2003) Eur. J. Biochem. 270 589–599 Occurrence Handle10.1046/j.1432-1033.2003.03426.x Occurrence Handle12581199

    Article  PubMed  Google Scholar 

  • N. B. Egen M. Bliss M. Mayersohn S. M. Owens L. Arnold M. Bier (1988) Anal. Biochem. 172 488–494 Occurrence Handle10.1016/0003-2697(88)90472-1 Occurrence Handle3189790

    Article  PubMed  Google Scholar 

  • F. Fortis P. Girot O. Brieau E. Boschetti A. Castagna P.G. Righetti (2005a) Proteomics 5 620–628 Occurrence Handle10.1002/pmic.200401113

    Article  Google Scholar 

  • F. Fortis P. Girot O. Brieau A. Castagna P.G. Righetti E. Boschetti (2005b) Proteomics 5 629–638 Occurrence Handle10.1002/pmic.200401112

    Article  Google Scholar 

  • M. Fountoulakis J. F. Juranville (2003) Anal. Biochem. 313 267–282 Occurrence Handle10.1016/S0003-2697(02)00617-6 Occurrence Handle12605864

    Article  PubMed  Google Scholar 

  • A. Görg G. Boguth A. Köpf G. Reil H. Parlar W. Weiss (2002) Proteomics 2 1652–1657 Occurrence Handle10.1002/1615-9861(200212)2:12<1652::AID-PROT1652>3.0.CO;2-3 Occurrence Handle12469334

    Article  PubMed  Google Scholar 

  • S. P. Gygi G. L. Corthals Y. Zhang Y. Rochon R. Aebersold (2000) Proc. Natl. Acad. Sci. USA 97 9390–9395 Occurrence Handle10.1073/pnas.160270797 Occurrence Handle10920198

    Article  PubMed  Google Scholar 

  • Hannig, K. (1967) In: Electrophoresis: Theory, Methods and Applications, Vol. 2 (M. Bier, ed.), Academic Press, New York, pp. 423–471.

  • K. Hannig (1982) Electrophoresis 3 235–242 Occurrence Handle10.1002/elps.1150030502

    Article  Google Scholar 

  • M. Hayakawa Y. Hosogi H. Takiguchi T. Shiroza Y. Shibata K. Hiratsuka M. Kiyama-Kishikawa S. Hamajima Y. Abiko (2003) Anal. Biochem. 313 60–67 Occurrence Handle10.1016/S0003-2697(02)00509-2 Occurrence Handle12576059

    Article  PubMed  Google Scholar 

  • B. R. Herbert P. G. Righetti (2000) Electrophoresis 21 3639–3648 Occurrence Handle10.1002/1522-2683(200011)21:17<3639::AID-ELPS3639>3.0.CO;2-V Occurrence Handle11271482

    Article  PubMed  Google Scholar 

  • B. Herbert S. K. Pedersen J. L. Harry L. Sebastian J. Grinyer M. D. Traini J. T. McCarthy M. R. Wilkins A. A. Gooley P. G. Righetti N. H. Packer K. L. Williams (2003) PharmaGenomics 3 22–36

    Google Scholar 

  • Herbert, B., Righetti, P. G., McCarthy, J., Grinyer, J., Castagna, A., Laver, M., Durack, M., Rummery, G., Harcourt, R. and Williams, K. L. (2004) In: Purifying Proteins for Proteomics (R. J. Simpson, ed.), Cold Spring Harbor Lab. Press, Cold Spring Harbor, pp. 431–442.

  • S. Hjertén (1967) Chromatogr. Rev. 9 122–219 Occurrence Handle10.1016/0009-5907(67)80003-6 Occurrence Handle4883163

    Article  PubMed  Google Scholar 

  • A. C. Hochstrasser R. W. James D. Pometta D. Hochstrasser (1991) Appl. Theor. Electrophor. 1 333–337 Occurrence Handle1932203

    PubMed  Google Scholar 

  • P. Hoffmann H. Ji R. L. Moritz L. M. Connolly D. F. Frecklington M. J. Layton J. S. Eddes R. J. Simpson (2001) Proteomics 1 807–818 Occurrence Handle10.1002/1615-9861(200107)1:7<807::AID-PROT807>3.3.CO;2-Y Occurrence Handle11503205

    Article  PubMed  Google Scholar 

  • Z. S. Horvàth A. A. Gooley C. W. Wrigley J. Margolis K. L. Williams (1996) Electrophoresis 17 224–226 Occurrence Handle10.1002/elps.1150170138 Occurrence Handle8907545

    Article  PubMed  Google Scholar 

  • S. Hoving H. Voshol J. Oostrum Particlevan (2000) Electrophoresis 21 2617–2621 Occurrence Handle10.1002/1522-2683(20000701)21:13<2617::AID-ELPS2617>3.0.CO;2-C Occurrence Handle10949138

    Article  PubMed  Google Scholar 

  • L. A. Huber K. Pfaller I. Vietor (2003) Circulation Res. 92 962–968 Occurrence Handle10.1161/01.RES.0000071748.48338.25 Occurrence Handle12750306

    Article  PubMed  Google Scholar 

  • C. F. Ivory (2004) Electrophoresis 25 360–374 Occurrence Handle10.1002/elps.200305753 Occurrence Handle14743489

    Article  PubMed  Google Scholar 

  • H. J. Issaq T. P. Conrads G. M. Janini T. D. Veenstra (2002) Electrophoresis 23 3048–3061 Occurrence Handle10.1002/1522-2683(200209)23:17<3048::AID-ELPS3048>3.0.CO;2-L Occurrence Handle12207315

    Article  PubMed  Google Scholar 

  • M. Jonsson H. Rilbe (1980) Electrophoresis 1 3–14 Occurrence Handle10.1002/elps.1150010103

    Article  Google Scholar 

  • E. Jung M. Heller J. C. Sanchez D. F. Hochstrasser (2000) Electrophoresis 21 3369–3377 Occurrence Handle10.1002/1522-2683(20001001)21:16<3369::AID-ELPS3369>3.0.CO;2-7 Occurrence Handle11079557

    Article  PubMed  Google Scholar 

  • H. Kobayashi K. Shimamura T. Akaida E. Sakano N. Tajima J. Funazaki H. Suzuki E. Shinohara (2003) J. Chromatogr. A 990 169–178 Occurrence Handle10.1016/S0021-9673(02)01964-7

    Article  Google Scholar 

  • R. Kuhn H. Wagner (1989) J. Chromatogr. 481 343–350 Occurrence Handle10.1016/S0021-9673(01)96777-9 Occurrence Handle2687308

    Article  PubMed  Google Scholar 

  • S. Lalwani E. Shave H. C. Fleisher K. Nzeadibe M. B. Busby G. Vigh (2004a) Electrophoresis 25 2128–2138 Occurrence Handle10.1002/elps.200305944

    Article  Google Scholar 

  • S. Lalwani E. Shave G. Vigh (2004b) Electrophoresis 25 3323–3330 Occurrence Handle10.1002/elps.200406045

    Article  Google Scholar 

  • P. Lescuyer D. F. Hochstrasser J. -C. Sanchez (2004) Electrophoresis 25 1125–1135 Occurrence Handle10.1002/elps.200305792 Occurrence Handle15095456

    Article  PubMed  Google Scholar 

  • V. L. Locke T. S. Gibson T. M. Thomas G. L. Corthals D. B. Rylatt (2002) Proteomics 2 1254–1260 Occurrence Handle10.1002/1615-9861(200209)2:9<1254::AID-PROT1254>3.0.CO;2-A Occurrence Handle12362343

    Article  PubMed  Google Scholar 

  • M. F. Lopez (2000) Electrophoresis 21 1082–1093 Occurrence Handle10.1002/(SICI)1522-2683(20000401)21:6<1082::AID-ELPS1082>3.0.CO;2-E Occurrence Handle10786882

    Article  PubMed  Google Scholar 

  • J. Margolis G. Corthals Z. S. Horvàth (1995) Electrophoresis 16 98–100 Occurrence Handle10.1002/elps.1150160117 Occurrence Handle7737097

    Article  PubMed  Google Scholar 

  • P. E. Michel P. Reymond I. L. Arnaud J. Josserand H. H. Girault J. S. Rossier (2003) Electrophoresis 24 3–11 Occurrence Handle10.1002/elps.200390030 Occurrence Handle12652567

    Article  PubMed  Google Scholar 

  • S. K. Pedersen J. L. Harry L. Sebastian J. Baker M. D. Traini J. T. McCarthy A. Manoharan M. R. Wilkins A. A. Gooley P. G. Righetti N. H. Packer K. L. Williams B. Herbert (2003) J. Proteome Res. 2 303–312 Occurrence Handle10.1021/pr025588i Occurrence Handle12814269

    Article  PubMed  Google Scholar 

  • R. Pieper C. L. Gatlin A. J. Makusky P. S. Russo C. R. Schatz S. S. Miller Q. Su A. M. McGrath M. A. Estock P. P. Parmar M. Zhao S. T. Huang J. Zhou F. Wang R. Esquer-Blasco N. L. Anderson J. Taylor S. Steiner (2003) Proteomics 3 1345–1364 Occurrence Handle10.1002/pmic.200300449 Occurrence Handle12872236

    Article  PubMed  Google Scholar 

  • M. C. Pietrogrande N. Marchetti F. Dondi P. G. Righetti (2002) Electrophoresis 23 283–291 Occurrence Handle10.1002/1522-2683(200202)23:2<283::AID-ELPS283>3.0.CO;2-5 Occurrence Handle11840537

    Article  PubMed  Google Scholar 

  • M. C. Pietrogrande N. Marchetti F. Dondi P. G. Righetti (2003) Electrophoresis 24 217–224 Occurrence Handle10.1002/elps.200390018 Occurrence Handle12652594

    Article  PubMed  Google Scholar 

  • H.G. Rammensee (2004) Nature 427 203–204 Occurrence Handle10.1038/427203a Occurrence Handle14724617

    Article  PubMed  Google Scholar 

  • P.G. Righetti (1983) Isoelectric Focusing: Theory, Methodology and Applications Elsevier Amsterdam 129–136

    Google Scholar 

  • P. G. Righetti E. Wenisch M. Faupel (1989) J. Chromatogr. 475 293–309 Occurrence Handle10.1016/S0021-9673(01)89684-9

    Article  Google Scholar 

  • P. G. Righetti E. Wenisch A. Jungbauer H. Katinger M. Faupel. (1990) J. Chromatogr. 500 681–696 Occurrence Handle10.1016/S0021-9673(00)96103-X Occurrence Handle2329157

    Article  PubMed  Google Scholar 

  • P. G. Righetti (1990) Immobilized pH Gradients: Theory and Methodology Elsevier Amsterdam 1–400

    Google Scholar 

  • Righetti, P. G., Faupel, M. and Wenisch, E. (1992) In: Advances in Electrophoresis, Vol. 5 (A. Chrambach, M. J. Dunn and B. J. Radola, eds.), VCH, Weinheim, pp. 159–200.

  • P. G. Righetti A. Castagna B. Herbert (2001) Anal. Chem. 73 320A–326A Occurrence Handle11403326

    PubMed  Google Scholar 

  • P. G. Righetti A. Castagna B. Herbert F. Reymond J. S. Rossier (2003a) Proteomics 3 1397–1407 Occurrence Handle10.1002/pmic.200300472

    Article  Google Scholar 

  • Righetti, P. G., Castagna, A., and Hamdan, M. (2003b) In: Advances in Chromatography, Vol. 42 (P. R. Brown and E. Grushka, eds.), M. Dekker, New York, pp. 270–321.

  • A. Ros M. Faupel H. Mees J. V. Oostrum R. Ferrigno F. Reymond P. Michel J. S. Rossier H. H. Girault (2002) Proteomics 2 151–156 Occurrence Handle10.1002/1615-9861(200202)2:2<151::AID-PROT151>3.0.CO;2-9 Occurrence Handle11840561

    Article  PubMed  Google Scholar 

  • T. Q. Shang J. M. Ginter M. V. Johnston B. S. Larsen C. N. McEwen (2003) Electrophoresis 24 2359–2368 Occurrence Handle10.1002/elps.200305502 Occurrence Handle12874871

    Article  PubMed  Google Scholar 

  • C. Southan (2004) Proteomics 4 1712–1726 Occurrence Handle10.1002/pmic.200300700 Occurrence Handle15174140

    Article  PubMed  Google Scholar 

  • C. Stannard L. R. Brown J. Godovac-Zimmermann (2004) Curr. Proteomics 1 13–25

    Google Scholar 

  • A. Tan A. Pashkova L. Zang F. Foret B. L. Karger (2002) Electrophoresis 23 3599–3607 Occurrence Handle10.1002/1522-2683(200210)23:20<3599::AID-ELPS3599>3.0.CO;2-M Occurrence Handle12412130

    Article  PubMed  Google Scholar 

  • N. I. Tracy C. F. Ivory (2004) Electrophoresis 25 1748–1757 Occurrence Handle10.1002/elps.200305832 Occurrence Handle15213972

    Article  PubMed  Google Scholar 

  • D. B. Wall M. T. Kachman S. Gong R. Hinderer S. Parus D. E. Misek S. M. Hanash D. M. Lubman (2000) Anal. Chem. 72 1099–1111 Occurrence Handle10.1021/ac991332t Occurrence Handle10740846

    Article  PubMed  Google Scholar 

  • H. Wang M. T. Kachman D. R. Schwartz K. R. Cho D. M. Lubman (2002) Electrophoresis 23 3168–3181 Occurrence Handle10.1002/1522-2683(200209)23:18<3168::AID-ELPS3168>3.0.CO;2-A Occurrence Handle12298089

    Article  PubMed  Google Scholar 

  • G. Weber M. Islinger P. Weber C. Eckerskorn A. Volkl (2004) Electrophoresis 25 1735–1747 Occurrence Handle10.1002/elps.200305834 Occurrence Handle15213971

    Article  PubMed  Google Scholar 

  • P. Wenger M. Zuanni Particlede P. Javet C. Gelfi P. G. Righetti (1987) J. Biochem. Biophys. Methods 14 29–43 Occurrence Handle10.1016/0165-022X(87)90004-2 Occurrence Handle3693792

    Article  PubMed  Google Scholar 

  • J. A. Westbrook J. X. Yan R. Wait S. Y. Welson M. J. Dunn (2001) Electrophoresis 22 2865–2871 Occurrence Handle10.1002/1522-2683(200108)22:14<2865::AID-ELPS2865>3.0.CO;2-Y Occurrence Handle11565781

    Article  PubMed  Google Scholar 

  • R. Wildgruber A. Harder C. Obermeier G. Boguth W. Weiss S. J. Fey P. M. Larsen A. Goerg (2000) Electrophoresis 21 2610–2616 Occurrence Handle10.1002/1522-2683(20000701)21:13<2610::AID-ELPS2610>3.0.CO;2-H Occurrence Handle10949137

    Article  PubMed  Google Scholar 

  • Z. Xiao T. P. Conrads D. A. Lucas G. M. Janini C. F. Schaefer K. H. Buetow H. J. Issaq T. D. Veenstra (2004) Electrophoresis 25 128–133 Occurrence Handle10.1002/elps.200305700 Occurrence Handle14730577

    Article  PubMed  Google Scholar 

  • Zhu, K., Yan, F., O'Neil, K. A., Hamler, R., Lin, L., Barder, T. J., and Lubman, D. M. (2003) Curr. Prot. Protein Sci. :2331–23328.

  • Y. Zhu D. M. Lubman (2004) Electrophoresis 25 949–958 Occurrence Handle10.1002/elps.200305779 Occurrence Handle15095432

    Article  PubMed  Google Scholar 

  • G. V. Zilberstein E. M. Baskin S. Bukshpan (2003) Electrophoresis 24 3735–3744 Occurrence Handle10.1002/elps.200305663 Occurrence Handle14613199

    Article  PubMed  Google Scholar 

  • G. V. Zilberstein E. M. Baskin S. Bukshpan L. E. Korol (2004a) Electrophoresis 25 3643–3651 Occurrence Handle10.1002/elps.200406117

    Article  Google Scholar 

  • G. V. Zilberstein L. E. Korol S. Bukshpan E. M. Baskin (2004b) Proteomics 4 2533–2540 Occurrence Handle10.1002/pmic.200300794

    Article  Google Scholar 

  • H. Zischka G. Weber P. J. A. Weber A. Posch R. J. Braun D. Buhringer U. Schneider M. Nissum T. Meitinger M. Ueffing C. Eckerskorn (2003) Proteomics 3 906–916 Occurrence Handle10.1002/pmic.200300376 Occurrence Handle12833514

    Article  PubMed  Google Scholar 

  • X. Zuo D. W. Speicher (2002) Proteomics 2 58–68 Occurrence Handle10.1002/1615-9861(200201)2:1<58::AID-PROT58>3.3.CO;2-7 Occurrence Handle11788992

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Industrial and Agricultural Biotechnologies, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy

    Pier Giorgio Righetti & Annalisa Castagna

  2. Proteome Systems, 35 Waterloo Rd, North Ryde, 2113, Sydney, NSW, Australia

    Ben Herbert

  3. Laboratory on Physiopathology of Uremia, G. Gaslini Children’s Hospital, 16148, Genova, Italy

    Giovanni Candiano

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  1. Pier Giorgio Righetti
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  2. Annalisa Castagna
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  3. Ben Herbert
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  4. Giovanni Candiano
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Correspondence to Pier Giorgio Righetti.

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Righetti, P.G., Castagna, A., Herbert, B. et al. How to Bring the “Unseen” Proteome to the Limelight via Electrophoretic Pre-Fractionation Techniques. Biosci Rep 25, 3–17 (2005). https://doi.org/10.1007/s10540-005-2844-2

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