A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment

Analytica Chimica Acta

Volumn 836, Issue , 2014, Pages 1-17

  Moreda Piñeiro, Antonio ^a   García Otero, Natalia ^a   Bermejo Barrera, Pilar ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

Isoelectric focusing; Offgel electrophoresis; Peptide; Protein

Indexed keywords

MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; PROTEINS;

CHROMATOGRAPHIC TECHNIQUES; DEVELOPMENT AND APPLICATIONS; DIMENSIONAL ANALYSIS; ELECTROPHORESIS DEVICES; ISOELECTRIC FOCUSING; MULTIDIMENSIONAL PROTEINS; PROTEIN FRACTIONATION; PROTEIN IDENTIFICATION;

ELECTROPHORESIS;

TRYPSIN; ISOPROTEIN; METAL; PEPTIDE; PROTEIN;

CHEMICAL COMPOSITION; CHROMATOGRAPHY; DESALINATION; ELECTROPHORESIS; FRACTIONATION; GEL ELECTROPHORESIS; ISOELECTRIC FOCUSING; MASS SPECTROMETRY; OFFGEL ELECTROPHORESIS; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN DETERMINATION; PROTEIN INTERACTION; REVIEW; CHEMISTRY; DEVICES; PROCEDURES; TANDEM MASS SPECTROMETRY; TRENDS;

CHEMICAL FRACTIONATION; ELECTROPHORESIS; ISOELECTRIC FOCUSING; METALS; PEPTIDES; PROTEIN ISOFORMS; PROTEINS; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 84903477808     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2014.04.053     Document Type: Review

References (107)

1. Westermeier R., Naven T., Höpker H.-R. Proteomics in Practice: A Guide to Successful Experimental Design 2008, 1-15. Wiley-VCH, Weinheim, Germany.
2. Gorg A., Weiss W., Dunn M.J. Proteomics 2004, 4:3665-3685.
3. Imai K., Koshiyama A., Nakata K. Biomed. Chromatogr. 2011, 25:59-64.
4. Issaq H.J., Veenstra T.D. Biotechniques 2008, 44:697-700.
5. Westermeier R. Electrophoresis in Practice 2005, 91-119. Wiley-VCH, Weinheim, Germany.
6. Tang J., Gao M., Deng C., Zhang X. J. Chromatogr. B 2008, 866:123-132.
7. Roe M.R., Griffin T.J. Proteomics 2006, 6:4678-4687.
8. Hörth P., Miller C.A., Preckel T., Wenz C. Mol. Cell. Proteomics 2006, 5:1968-1974.
9. Manadas B., Mendes V.M., English J., Dunn M.J. Expert Rev. Proteomics 2010, 7:655-663.
10. Stoyanov A. Electrophoresis 2012, 33:3281-3290.
11. Westermeier R. Electrophoresis in Practice 2005, 197-208. Wiley-VCH, Weinheim, Germany.
12. Lopez M.F. Non-equilibrium pH gel electrophoresis (NEPHGE). The Protein Protocols Handbook 2002, 181-182. Humana Press Inc., Totowa, NJ, USA. J.M. Walker (Ed.).
13. Hjertén S. Chromatogr. Rev. 1967, 9:122-219.
14. Hoffmann P., Ji H., Moritz R.L., Connolly L.M., Frecklington D.F., Layton M.J., Eddes J.S., Simpson R.J. J. Proteomics 2001, 1:807-818.
15. Zischka H., Weber G., Weber P.J.A., Posch A., Braun R.J., Buhringer D., Schneider U., Nissum M., Meitinger T., Ueffing M., Eckerskorn C. Proteomics 2003, 3:906-916.
16. Moritz R.L., Ji H., Schutz F., Connolly L.M., Kapp E.A., Speed T.P., Simpson R.J. Anal. Chem. 2004, 76:4811-4824.
17. Weber G., Islinger M., Weber P., Eckerskorn C., Volkl A. Electrophoresis 2004, 25:1735-1747.
18. Moritz R.L., Simpson R.J. Nat. Methods 2005, 2:863-873.
19. Jonsson M., Rilbe H. Electrophoresis 1980, 1:3-14.
20. Bier M. Electrophoresis 1998, 19:1057-1063.
21. Righetti P.G., Castagna A., Herbert B., Reymond F., Rossier J.S. Proteomics 2003, 3:1397-1407.
22. Wall D.B., Kachman M.T., Gong S.Y., Hinderer R., Parus S., Misek D.E., Hanash S.M., Lubman D.M. Anal. Chem. 2000, 72:1099-1111.
23. Ayala A., Parrado J., Machado A. Appl. Biochem. Biotechnol. 1998, 69:11-16.
24. Righetti P.G., Wenisch E., Faupel M.J. J. Chromatogr. 1989, 475:293-309.
25. Herbert B., Righetti P.G. Electrophoresis 2000, 21:3639-3648.
26. Pedersen S.K., Harry J.L., Sebastian L., Baker J., Traini M.D., McCarthy J.T., Manoharan A., Wilkins M.R., Gooley A.A., Righetti P.G., Packer N.H., Williams K.L., Herbert B.R. J. Proteome Res. 2003, 2:303-311.
27. Ros A., Faupel M., Mees H., van Oostrum J., Ferrigno R., Reymond F., Michel P., Rossier J.S., Girault H.H. Electrophoresis 2002, 23:3253-3261.
28. Arnaud I.L., Josserand J., Rossier J.S., Girault H.H. Electrophoresis 2002, 23:3253-3261.
29. Lam H.-T., Josserand J., Lion N., Girault H.H. J. Proteome Res. 2007, 6:1666-1676.
30. Michel P.E., Reymond F., Arnaud I.L., Josserand J., Girault H.H., Rossier J.S. Electrophoresis 2003, 24:3-11.
31. Heller M., Michel P.E., Morier P., Crettaz D., Wenz C., Tissot J.-D., Reymond F., Rossier J.S. Electrophoresis 2005, 26:1174-1188.
32. Krishnan S., Gaspari M., della Corte A., Bianchi P., Crescente M., Cerletti C., Torella D., Indolfi C., de Gaetano M., Rotilio D., Cuda G. Electrophoresis 2011, 32:686-695.
33. Stalder D., Haeberli A., Heller M. Proteomics 2008, 8:414-424.
34. Schafer A., von Toerne C., Becker S., Sarioglu H., Neschen S., Kahle M., Hauck S.M., Ueffing M. Anal. Chem. 2012, 84:8853-8862.
35. Manadas B., English J.A., Wynne K.J., Cotter D.R., Dunn M.J. Proteomics 2009, 9:5194-5198.
36. Chiu C.-W., Chang C.-L., Chen S.-F. J. Sep. Sci. 2012, 35:3293-3301.
37. García-Otero N., Peña-Vazquez E., Barciela-Alonso M.C., Bermejo-Barrera P., Moreda-Piñeiro A. Anal. Chem. 2013, 85:5909-5916.
38. Keidel E.-M., Dosch D., Brunner A., Kellermann J., Lottspeich F. Electrophoresis 2011, 32:1659-1666.
39. Tobolkina E., Cortés-Salazar F., Momotenko D., Maillard J., Girault H.H. Electrophoresis 2012, 33:3331-3338.
40. Ang C.-S., Binos S., Knight M.I., Moate P.J., Cocks B.G., McDonagh M.B. J. Proteome Res. 2011, 10:5059-5069.
41. Mulvenna J., Hamilton B., Nagaraj S.H., Smyth D., Loukas A., Gorman J.J. Mol. Cel. Proteomics 2009, 8:109-121.
42. Gannon J., Ohlendieck K. Mol. Med. Rep. 2012, 5:993-1000.
43. Arrey T.N., Rietschel B., Papasotiriou D.G., Bornemann S., Baeumlisberger D., Karas M., Meyer B. Anal. Chem. 2010, 82:2145-2149.
44. Khalilpour A., Santhanam A., Wei L.C., Saadatnia G., Velusamy N., Osman S., Mohamad A.M., Noordin R. Asian Pac. J. Cancer Prev. 2013, 14:1635-1642.
45. O'Cualain R.D.M., Hyde J.E., Sims P.F.G. Malar. J. 2010, 9:286.
46. García-Otero N., Barciela-Alonso M.C., Moreda-Piñeiro A., Bermejo-Barrera P. Talanta 2013, 115:631-641.
47. Balasubramani M., Nakao C., Uechi G.T., Cardamone J., Kamath K., Leslie K.L., Balachandran R., Wilson L., Day B.W., Jordan M.A. Mutat. Res. 2011, 722:154-164.
48. Burgess J.A., Lescuyer P., Hainard A., Burkhard P.R., Turck N., Michel P., Rossier J.S., Reymond F., Hochstrasser D.F., Sanchez J.-C. J. Proteome Res. 2006, 5:1674-1681.
49. Mena M.L., Moreno-Gordaliza E., Moraleja I., Cañas B., Gómez-Gómez M.M. J. Chromatogr. A 2011, 1218:1281-1290.
50. Michel P.E., Crettaz D., Morier P., Heller M., Gallot D., Tissot J.-D., Reymond F., Rossier J.S. Electrophoresis 2006, 27:1169-1181.
51. Mun J., Kim Y.-H., Yu J., Bae J., Noh D.-Y., Yu M.-H., Lee C. Electrophoresis 2010, 31:3428-3436.
52. Scruggs S.B., Reisdorph R., Armstrong M.L., Warren C.M., Reisdorph N., Solaro R.J., Buttrickm P.M. Mol. Cell. Proteomics 2010, 9:1804-1818.
53. Watanabe J., Charles-Schoeman C., Miao Y., Elashoff D., Lee Y.Y., Katselis G., Lee T.D., Reddy S.T. Arthritis Rheum. 2012, 64:1828-1837.
54. Zhang Y., Li Y., Qiu F., Qiu Z. Electrophoresis 2010, 31:3797-3807.
55. Chandramouli K.H., Agrawal P., Thimmaiah K.N. Curr. Proteomics 2009, 6:43-50.
56. Kuhn J.F., Hoerth P., Hoehn S.T., Preckel T., Tomer K.B. Electrophoresis 2006, 27:1584-1597.
57. Busnel J.-M., Lion N., Girault H.H. Anal. Chem. 2007, 79:5949-5955.
58. Pourhaghighi M.R., Karzand M., Girault H.H. Anal. Chem. 2011, 83:7676-7681.
59. Chen X., Simon E.S., Xiang Y., Kachman M., Andrews P.C., Wang Y. J. Biol. Chem. 2010, 285:7197-7207.
60. Collins B.C., Miller C.A., Sposny A., Hewitt P., Wells M., Gallagher W.M., Pennington S.R. Mol. Cell. Proteomics 2012, 11(8):394-410.
61. Ho J.H., Lee O.K., Fu Y.-J., Shih H.-T., Tseng C.-Y., Chung C.-C., Han C.-L., Chen Y.-J. J. Proteome Res. 2013, 12:1120-1133.
62. Ambekar A.S., Nirujogi R.S., Srikanth S.M., Chavan S., Kelkar D.S., Hinduja I., Zaveri K., Prasad T.S.K., Harsha H.C., Pandey A., Mukherjee S. J. Proteomics 2013, 87:68-77.
63. Chenau J., Michelland S., de Fraipont F., Josserand V., Coll J.-L., Favrot M.-C., Seve M. J. Proteome Res. 2009, 8:4579-4591.
64. Gasilova N., Qiao L., Momotenko D., Pourhaghighi M.R., Girault H.H. Anal. Chem. 2013, 85:6254-6263.
65. He W., Huang C., Luo G., Prà I.D., Feng J., Chen W., Ma L., Wang Y., Chen X., Tan J., Zhang X., Armato U., Wu J. Proteomics 2012, 12:1059-1072.
66. Nagano K., Shinkawa T., Yabuki N., Mutoh H., Inomata N., Watanabe Y., Ashihara M., Nagahashi S., Ishii N., Aoki Y., Haramura M. J. Proteomics 2011, 74:319-326.
67. Vaezzadeh A.R., Briscoe A.C., Steen H., Lee R.S. J. Proteome Res. 2010, 9:6082-6089.
68. Aziz A., Zhang W., Li J., Loukas A., McManus D.P., Mulvenna J. J. Proteomics 2011, 74:1560-1572.
69. Mulvenna J., Moerte L., Jones M.K., Nawaratna S., Lovas E.M., Gobert G.N., Colgrave M., Jones A., Loukas A., McManus D.P. Int. J. Parasitol. 2010, 40:543-554.
70. Mulvenna J., Sripa B., Brindley P.J., Gorman J., Jones M.K., Colgrave M.L., Jones A., Nawaratna S., Laha T., Suttiprapa S., Smout M.J., Loukas A. Proteomics 2010, 10:1063-1078.
71. Elschenbroich S., Ignatchenko V., Sharma P., Schmitt-Ulms G., Gramolini A.O., Kislinger T. J. Proteome Res 2009, 8:4860-4869.
72. Perez-Riverola Y., Sánchez A., Ramos Y., Schmidt A., Müller M., Betancourt L., González L.J., Vera R., Padron G., Besada V. J. Proteomics 2011, 74:2071-2082.
73. Antberg L., Cifani P., Sandin M., Levander F., James P. J. Proteome Res. 2012, 11:2644-2652.
74. Bonzon-Kulichenko E., Pérez-Hernández D., Núñez E., Martínez-Acedo P., Navarro P., Trevisan-Herraz M., Ramos M.C., Sierra S., Martínez-Martínez S., Ruiz-Meana M., Miró-Casas E., García-Dorado D., Redondo J.M., Burgos J.S., Vázquez J. Mol. Cell. Proteomics 2011, 1-14. 10.1074/mcp.M110.003335.
75. Besson D., Pavageau A.-H., Valo I., Bourreau A., Bélanger A., Eymerit-Morin C., Moulière A., Chassevent A., Boisdron-Celle M., Morel A., Solassol J., Campone M., Gamelin E., Barré B., Coqueret O., Guette C. Mol. Cell. Proteomics 2011, 1-14. 10.1074/mcp.M111.009712.
76. Cao Z., Tang H.-Y., Wang H., Liu Q., Speicher D.W. J. Proteome Res. 2012, 11:3090-3100.
77. Elschenbroich S., Ignatchenko V., Clarke B., Kalloger S.E., Boutros P.C., Gramolini A.O., Shaw P., Jurisica I., Kislinger T. J. Proteome Res. 2011, 10:2286-2299.
78. Ernoult E., Bourreau A., Gamelin E., Guette C. J. Biomed. Biotechnol. 2010, Article ID 927917.
79. Waller L.N., Shores K., Knapp D.R. J. Proteome Res. 2008, 7:4577-4584.
80. Heller M., Ye M.-L., Michel P.E., Morier P., Stalder D., Jünger M.A., Aebersold R., Reymond F., Rossier J.S. J. Proteome Res. 2005, 4:2273-2282.
81. Austin R.J., Chang D.K., Holstein C.A., Lee L.-W., Risler J., Wang J.H., Adams L., Krusberski N.B., Martin D.B. Proteomics 2012, 12:2078-2083.
82. Dayon L., Turck N., Kienle S., Schulz-Knappe P., Hochstrasser D.F., Scher A., Sanchez J.-C. Anal. Chem. 2010, 82:848-858.
83. Paulo J.A., Kadiyala V., Banks P.A., Conwell D.L., Steen H. Genomics Proteomics Bioinformatics 2013, 11:105-113.
84. Warren C.M., Geenen D.L., Helseth D.L., Xu H., Solaro R.J. J. Proteomics 2010, 73:1551-1561.
85. Rappsilber J., Mann M., Ishihama Y. Nat. Protoc. 2007, 2:1896-1906.
86. Barbhuiya M.A., Sahasrabuddhe N.A., Pinto S.M., Muthusamy B., Singh T.D., Nanjappa V., Keerthikumar S., Delanghe H.C.H., Jalaj V., Gupta S., Shrivastav B.R., Tiwari P.K., Pandey A. Proteomics 2011, 11:4443-4453.
87. Fraterman S., Zeiger U., Khurana T.S., Rubinstein N.A., Wilm M. Proteomics 2007, 7:3404-3416.
88. Wong C.C.L., Cociorva D., Miller C.A., Schmidt A., Monell C., Aebersold R., Yates J.R. J. Proteome Res. 2013, 12:763-770.
89. Wiśniewski J.R., Zougman A., Nagaraj N., Mann M. Nat. Methods 2009, 6:359-362.
90. Wiśniewski J.R., Nagaraj N., Zougman A., Gnad F., Mann M. J. Proteome Res. 2010, 9:3280-3289.
91. Wiśniewski J.R., Zougman A., Mann M. J. Proteome Res. 2009, 8:5674-5678.
92. Zielinska D.F., Gnad F., Wiśsniewski J.R., Mann M. Cell 2010, 141:897-907.
93. Ostasiewicz P., Zielinska D.F., Mann M., Wiśniewski J.R. J. Proteome Res. 2010, 9:3688-3700.
94. McDowell G.S., Gaun A., Steen H. J. Proteome Res. 2013, 12:3809-3812.
95. Abdallah C., Sergeant K., Guillier C., Dumas-Gaudot E., Leclercq C.C., Renaut J. Proteome Sci. 2012, 10:37.
96. Ma C., Zhao X., Han H., Tong W., Zhang Q., Qin P., Chang C., Peng B., Ying W., Qian X. Electrophoresis 2013, 34:2440-2450.
97. Surowiec I., Koistinen K.M., Fraser P.D., Bramley P.M. Meat Sci. 2011, 89:233-237.
98. Sentandreu M.A., Fraser P.D., Halket J., Patel R., Bramley P.M. J. Proteome Res. 2010, 9:3374-3383.
99. Meisrimler C.-N., Lüthje S. J. Proteomics 2012, 75:2550-2562.
100. Konecna H., Muller L., Dosoudilova H., Potesil D., Bursikova J., Sedo O., Marova I., Zdrahal Z. J. Agric. Food Chem. 2012, 60:2418-2426.
101. Ernoult E., Gamelin E., Guette C. Proteome Sci. 2008, 6(27).
102. Chenau J., Michelland S., Sidibe J., Seve M. Proteome Sci. 2008, 6:9.
103. Hubner N.C., Ren S., Mann M. Proteomics 2008, 8:4862-4872.
104. Yang Y., Qiang X., Owsiany K., Zhang S., Thannhauser T.W., Li L. J. Proteome Res. 2011, 10:4647-4660.
105. Essader A.S., Cargile B.J., Bundy J.L., Stephenson J.L. Proteomics 2005, 5:24-34.
106. Jiménez M.S., Rodríguez L., Gómez M.T., Castillo J.R. Talanta 2010, 81:241-247.
107. García-Otero N., Barciela-Alonso M.C., Bermejo-Barrera P., Moreda-Piñeiro A., Jiménez M.S., Gómez M.T., Castillo J.R. Anal. Chim. Acta 2013, 804:59-65.