Free-flow electrophoresis in proteome sample preparation

Proteomics

Volumn 14, Issue 4-5, 2014, Pages 629-636

  Wildgruber, Robert ^a   Weber, Gerhard ^a   Wise, Petra ^b   Grimm, Daniela ^c   Bauer, Johann ^d  

^a FFE Service GmbH   (Germany)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c AARHUS UNIVERSITY   (Denmark)

^d MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Cell biology; Isoelectric point; Matrix free; Protein complex; Subcellular particles

Indexed keywords

PROTEOME;

ELECTROPHORESIS; EXOSOME; GOLGI COMPLEX; HUMAN; INTERVAL ZONE ELECTROPHORESIS; INTRACELLULAR SPACE; ISOTACHOPHORESIS; MITOCHONDRION; NONHUMAN; PEROXISOME; PHAGOSOME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEOMICS; REVIEW; SUBCELLULAR COMPARTMENT; SYNAPTOSOME; WHOLE CELL; ZONE ELECTROPHORESIS; GOLGI MEMBRANE;

CELL BIOLOGY; ISOELECTRIC POINT; MATRIX FREE; PROTEIN COMPLEX; SUBCELLULAR PARTICLES;

ANIMALS; CELL MEMBRANE; ELECTROPHORESIS; HUMANS; ISOELECTRIC FOCUSING; ORGANELLES; PROTEIN BIOSYNTHESIS; PROTEOME;

EID: 84896756881     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300253     Document Type: Review

References (86)

1. Hannig, K., Heidrich, H., Free-Flow Electrophoresis, GIT-Verlag, Darmstadt 1990.
2. Hannig, K., New aspects in preparative and analytical continuous free-flow cell electrophoresis. Electrophoresis 1982, 3, 235-243.
3. Krivankova, L., Bocek, P., Continuous free-flow electrophoresis. Electrophoresis 1998, 19, 1064-1074.
4. Bauer, J., Electrophoretic separation of cells. J. Chromatogr. 1987, 418, 359-383.
5. Canut, H., Bauer, J., Weber, G., Separation of plant membranes by electromigration techniques. J. Chromatogr. B. 1999, 722, 121-139.
6. Weber, G., Bocek, P., Optimized continuous flow electrophoresis. Electrophoresis 1996, 17, 1906-1910.
7. Bauer, J., Weber, G., Sodium chloride in preparative free flow electrophoresis: recent developments. Electrophoresis 1996, 17, 526-528.
8. Weber, G., Bocek, P., Recent decelopments in preparative free flow isoelectric focusing. Electrophoresis 1998, 19, 1649-1653.
9. Weber, G., Bocek, P., Interval isotachophoresis for purification isolation of ionogenic species. Electrophoresis 1998, 19, 3090-3093.
10. Bondy, B., Bauer, J., Seuffert, I., Weber, G., Sodium chloride in separation medium enhances cell compatibility of free flow electrophoresisis. Electrophoresis 1995, 16, 92-97.
11. Islinger, M., Eckerskorn, C., Volkl, A., Free-flow electrophoresis in the proteomic era: a technique in flux. Electrophoresis 2010, 31, 1754-1763.
12. Moritz, R. L., Clippingdale, A. B., Kapp, E. A., Eddes, J. S. et al., Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins. Proteomics 2005, 5, 3402-3413.
13. Cox, J., Mann, M., Quantitative, high-resolution proteomics for data-driven systems biology. Ann. Rev. Biochem. 2011, 80, 273-299.
14. Vaudel, M., Sickmann, A., Martens, L., Current methods for global proteome identification. Expert Rev. Proteom. 2012, 9, 519-532.
15. Clamp, M., Fry, B., Kamal, M., Xie, X. et al., Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. USA 2007, 104, 19428-19433.
16. Sambuy, Y., Angelis, I., Ranaldi, G., Scarino, M. L. et al. The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics. Cell Biol. Toxicol. 2005, 21, 1-26.
17. Schonberger, J., Bauer, J., Spruss, T., Weber, G. et al., Establishment and characterization of the follicular thyroid carcinoma cell line ML-1. J. Mol. Med. 2000, 78, 102-110.
18. Thomas, J. W., Touchman, J. W., Blakesley, R. W., Bouffard, G. G. et al., Comparative analyses of multi-species sequences from targeted genomic regions. Nature 2003, 424, 788-793.
19. Reik, W., Stability and flexibility of epigentic gene regulation in mammalian development. Nature 2007, 447, 425-432.
20. Eberl, H. C., Mann, M., Vermeulen, M., Quantitative proteomics for epigenetics. Chembiochem 2011, 12, 224-234.
21. Tan, H. T., Lee, Y. H., Chung, M. C. M., Cancer proteomics. Mass Spectrom. Rev. 2012, 31, 583-605.
22. Uhlens, M., Bjorling, E., Agaton, C., Szigyarto, C. A. et al., A human proteins atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 2005, 4, 1920-1932.
23. Mehrishi, J. N., Bauer, J., Electrophoresis of cells and the biological relevance of surface charge. Electrophoresis 2002, 23, 1984-1994.
24. Weber, G., Grimm, D., Bauer, J., Application of binary buffer systems to free flow cell electrophoresis. Electrophoresis 2000, 21, 325-328.
25. Slivinsky, G. G., Hymer, W. C., Bauer, J., Morrison, D. R., Cellular electrophoretic mobility data: a first approach to a database. Electrophoresis 1997, 18, 1109-1119.
26. Bauer, J., Advances in cell separation: recent developments in counterflow centrifugal elutriation and continuous flow cell separation. J. Chromatogr. 1999, 722, 55-69.
27. Boogorad, L., Evolution of early eukaryotic cells: genomes, proteomes, and compartments. Photosyn. Res. 2008, 95, 11-21.
28. Satori, C. P., Kostal, V., Arriaga, E. A., Review on recent advances in the analysis of isolated organelles. Analyt. Chim. Acta 2012, 753, 8-18.
29. Amigorena, S., Drake, J. R., Webster, P., Mellman, I., Transient accumulation of new class II MHC molecules in a novel endocytic compartment in B lymphocytes. Nature 1994, 369, 113-120.
30. Henze, K., Martin, W., Evolutionary biology: essence of mitochondria. Nature 2003, 426, 127-128.
31. Hartwig, S., Feckler, C., Lehr, S., Wallbrecht, K. et al., A critical comparison between two classical and a kit-based method for mitochondria isolation. Proteomics 2009, 9, 3209-3214.
32. Braun, R. J., Kinkl, N., Zischka, H., Ueffing, M., 16-BAC/SDS-PAGE analysis of membrane proteins of yeast mitochondria purified by free flow electrophoresis. Methods Mol. Biol. 2009, 528, 83-107.
33. Eubel, H., Lee, C. P., Kuo, J., Meyer, E. H. et al., Free-flow electrophoresis for purification of plant mitochondria by surface charge. Plant J. 2007, 52, 583-594.
34. Lee, C. P., Eubel, H., O'Toole, N., Millar, A. H., Combining proteomics of root and shoot mitochondria and transcript analysis to define constitutive and variable components in plant mitochondria. Phytochemistry 2011, 72, 1092-1108.
35. Huang, S., Taylor, N. L., Narsai, R., Eubel, H. et al., Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. Plant Physiol. 2009, 149, 719-734.
36. Zischka, H., Braun, R. J., Marantidis, E. P., Buringer, D. et al., Differential analysis of Saccharomyces cerevisiae mitochondria by free flow electrophoresis. Mol. Cell. Proteomics 2006, 5, 2185-2200.
37. Thomas, S. N., Waters, K. M., Morgan, W. F., Yang, A. J. et al., Quantitative proteomic analysis of mitochondrial proteins reveals prosurvival mechanisms in the perpetuation of radiation-induced genomic instability. Free Radical Biol. Med. 2012, 53, 618-628.
38. de Duve, C., Evolution of the peroxisome. Ann. NY Acad. Sci. 1969, 168, 369-381.
39. Reumann, S., Toward a definition of the complete proteome of plant peroxisomes: where experimental proteomics must be complemented by bioinformatics. Proteomics 2011, 11, 1764-1779.
40. Kikuchi, M., Hatano, N., Yokota, S., Shimozawa, N. et al., Proteomic analysis of rat liver peroxisome. Presence of peroxisome-specific isozyme of Lon protease. J. Biol. Chem. 2004, 279, 421-428.
41. Islinger, M., Lüers, G. H., Li, K. W., Loos, M., Völkl, A., Rat liver peroxisomes after fibrate treatment: a survey using quantitative mass spectrometry. J. Biol. Chem. 2007, 282, 23055-23069.
42. Eubel, H., Meyer, E. H., Taylor, N. L., Bussell, J. D. et al., Novel proteins, putative membrane transporters, and an integrated metabolic network are revealed by quantitative proteomic analysis of Arabidopsis cell culture peroxisomes. Plant Physiol. 2008, 148, 1809-1829.
43. Islinger, M., Li, K. W., Loos, M., Liebler, S. et al., Peroxisomes from the heavy mitochondrial fraction: isolation by zonal free flow electrophoresis and quantitative mass spectrometrical characterization. J. Proteome Res. 2010, 9, 113-124.
44. Islinger, M., Abdolzade-Bavil, A., Liebler, S., Weber, G., Völkl, A., Assessing heterogeneity of peroxisomes: isolation of two subpopulations from rat liver. Methods Mol. Biol. 2012, 909, 83-96.
45. Nathan C., Neutrophils and immunity: challenges and opportunities. Nat. Rev. Immunol. 2006, 6, 173-182.
46. Jethwaney, D., Islam, M. R., Leidal, K. G., de Bernabe, D. B. V. et al., Proteomic analysis of plasma membrane and secretory vesicles from human neutrophils. Proteome Sci. 2007, 5, 12.
47. Lamb, F. S., Hook, J. S., Hilkin, B. M., Huber, J. N. et al., Endotoxin priming of neutrophils requires endocytosis and NADPH oxidase-dependent endosomal reactive oxygen species. J. Biol. Chem. 2012, 287, 12395-12404
48. Raiteri, L., Raiteri, M., Synaptosomes still viable after 25 years of superfusion. Neurochem. Res. 2000, 25, 1265-1274.
49. Islinger, M., Kirsch, J., Angermüller, S., Rotaru, R. et al., Subcellular fractionation of brain tissue using free-flow electrophoresis. Neuromethods, 2011, 57, 27-45.
50. Farquhar, M. G., Palade, G. E., The Golgi-apparatus (complex) (1954-1981) from artifact to center stage. J. Cell Biol. 1981, 91, S77-S103.
51. Parsons, H. T., Christiansen, K., Knierim, B., Carroll, A. et al., Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol. 2012, 159, 12-26.
52. Hathout, Y., Approaches to the study of the cell secretome. Expert Rev. Proteomics 2007, 4, 239-248.
53. Hu, L. L., Huang, T., Cai, Y. D., Chou, K. C., Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS ONE 2011, 6, e22989.
54. Grimm, D., Infanger, M., Westphal, K., Ulbrich, C. et al., A delayed type of three-dimensional growth of human endothelial cells under simulated weightlessness. Tissue Eng. Part A 2009, 15, 2267-2275.
55. Thery, C., Regnault, A., Garin, J., Wolfers, J. et al., Molecular characterization of dendritic cell-derived exosomes: selective accumulation of the heat shock protein hsc73. J. Cell Biol. 1999, 147, 599-610.
56. Weber, G., Bauer, J., Counterbalancing hydrodynamic sample distortion effects increases resolution of free-flow zone electrophoresis. Electrophoresis 1998, 19, 1104-1109.
57. Tunica, D. G., Yin, X., Sidibe, A., Stegemann, C. et al., Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS. Proteomics 2009, 9, 4991-4996.
58. Nissum, M., Kuhfuss, S., Hauptmann, M., Obermaier, C. et al., Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis. Proteomics 2007, 7, 4218-4227.
59. Wildgruber, R., Yi, J., Nissum, M., Eckerskorn, C., Weber, G., Free-flow electrophoresis system for plasma proteomic applications. Methods Mol. Biol. 2008, 424, 287-300.
60. Nissum, M., Foucher, A. L., Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis. Expert Rev. Proteomics 2008, 5, 571-587.
61. Hartwig, S., Kotzka, J., Müller, H., Müller-Wieland, D. et al., Enhancing mass spectrometry based serum profiling by a combination of free flow electrophoresis and ClinProt™. Arch. Physiol. Biochem. 2009, 115, 259-266.
62. Pernemalm, M., De Petris, L., Eriksson, H., Brandén, E. K. et al., Use of narrow-range peptide IEF to improve detection of lung adenocarcinoma markers in plasma and pleural effusion. Proteomics 2009, 9, 3414-3424.
63. Neustadt, M., Costina, V., Kupfahl, C., Buchheidt, D. et al., Characterization and identification of proteases secreted by Aspergillus fumigatus using free flow electrophoresis and MS. Electrophoresis 2009, 30, 2142-2150.
64. Xie, H., Rhodus, N. L., Griffin, R. J., Carlis, J. V., Griffin, T. J., A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry. Mol. Cell. Proteomics 2005, 4, 1826-1830.
65. Xie, H., Onsongo, G., Popko, J., de Jong, E. P. et al., Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry. Mol. Cell. Proteomics 2008, 7, 486-498.
66. Foucher, A. L., Craft, D. R., Gelfand, C. A., Application of free flow electrophoresis to the analysis of the urine proteome. Methods Mol. Biol. 2010, 641, 27-45.
67. Nissum, N., Wildgruber, R., Free-flow electrophoresis of the human urinary proteome. Methods Mol. Biol. 2008, 484, 131-144.
68. Adachi, J., Kumar, C., Zhang, Y., Olsen, J., Mann, M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 2006, 7, R80.
69. Raimondo, F., Morosi, L., Chinello, C., Magni, F., Pitto, M., Advances in membranous vesicle and exosome proteomics improving biological understanding and biomarker discovery. Proteomics 2011, 11, 709-720.
70. Thery, C., Zitvogel, L., Amigorena, S., Exosomes: composition, biogenesis and function. Nature Rev. Immunol. 2002, 2, 569-579.
71. Akers, J. C., Gonda, D., Kim, R., Carter, B. S., Chen, C. C., Biogenesis of extracellular vesicles (EV): exosomes, microvesicles, retrovirus-like vesicles, and apoptotic bodies. J. Neuro-Oncol. 2013, 113, 1-11.
72. Ma, X., Wildgruber, R., Bauer, J., Weber, G. et al., The use of sigmoid pH gradients in free-flow isoelectric focusing of human endothelial cell proteins. Electrophoresis 2012, 33, 1349-1355.
73. Nissum, M., Shehab, M. A., Sukop, U., Khosravi, J. M. et al., Functional and complementary phosphorylation state attributes of human insulin-like growth factor-binding protein-1 (IGFBP-1) isoforms resolved by free flow electrophoresis. Mol. Cell. Proteomics 2009, 8, 1424-1435.
74. Shehab, M. A., Iosef, C., Wildgruber, R., Sardana, G., Gupta, M. B., Phosphorylation of IGFBP-1 at discrete sites elicits variable effects on IGF-I receptor autophosphorylation. Endocrinology 2013, 154, 1130-1143.
75. Honig, B., Nicholls, A., Classical electrostatic in biology and chemistry. Science 1995, 268, 1144-1149.
76. von Heijne, G., Membrane-protein topology. Nature Rev. Mol. Cell Biol. 2006, 7, 909-918.
77. Behrens, C., Hartmann, K., Sunderhaus, S., Braun, H. P., Eubel, H., Approximate calculation and experimental derivation of native isoelectric points of membrane protein complexes of Arabidopsis chloroplasts and mitochondria. Biochim. Biophys. Acta- Biomembranes 2013, 1828, 1036-1046.
78. Obermaier, C., Jankowski, V., Schmutzler, C., Bauer, J. et al., Free-flow isoelectric focusing of proteins remaining in cell fragments following sonication of thyroid carcinoma cells. Electrophoresis 2005, 26, 2109-2116.
79. Pietsch, J., Kussian, R., Sickmann, A., Bauer, J. et al., Application of free-flow IEF to identify protein candidates changing under microgravity conditions. Proteomics 2010, 10, 904-913.
80. Pietsch, J., Riwaldt, S., Bauer, J., Sickmann, A. et al., Interaction of proteins identified in human thyroid cells. Int. J. Mol. Sci. 2013, 14, 1164-1178.
81. Pietsch, J., Sickmann, A., Weber, G., Bauer, J. et al., A proteomic approach to analysing spheroid formation of two human thyroid cell lines cultured on a random positioning machine. Proteomics 2011, 11, 2095-2104.
82. Pietsch, J., Sickmann, A., Weber, G., Bauer, J. et al. Metabolic enzyme diversity in different human thyroid cell lines and their sensitivity to gravitational forces. Proteomics 2012, 12, 2539-2546.
83. Pietsch, J., Bauer, J., Egli, M., Infanger, M. et al., The effect of weightlessness on the human mammalian cells. Current Mol. Med. 2011, 11, 350-364.
84. Hayes, M. J., Moss, S. E., Annexin 2 has a dual role as regulator and effector of v-SRC in cell trnasformation. J. Biol. Chem. 2009, 284, 10202-10210.
85. Justesen, B. H., Laursen, T., Weber, G., Fuglsang, A. T. et al., Isolation of monodisperse nanodisc-reconstituted membrane proteins using free flow electrophoresis. Analytical Chem. 2013, 85, 3497-3500.
86. Bauer, J., Weber, G., Interval carrier free electrophoresis for high resolution protein purification. J. Dispersion Sci. Technol. 1998, 19, 937-950.