Skip to main content

2D-DIGE as a Tool in Neuroproteomics

  • Protocol
  • First Online:
Neuroproteomics

Part of the book series: Neuromethods ((NM,volume 146))

  • 802 Accesses

Abstract

Neuroproteomics encompasses the study of all protein-related dynamics of the nervous system, not only on a morphological level in development and disease but also functional aspects of the process of learning as well as changes in clinical conditions like depression and addiction. Detection of these changes in protein abundance under defined conditions is the field of differential proteome analysis, with two-dimensional difference gel electrophoresis (2D-DIGE) currently being the most comprehensive technique to quantify these changes while retaining information about isoforms and posttranslational modifications. This chapter focusses on technical aspects of 2D-DIGE as well as a brief overview of successful applications of this technique in neuroproteomics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18(11):2071–2077

    Article  CAS  PubMed  Google Scholar 

  2. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S, Currie I (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3(1):36–44

    Article  CAS  PubMed  Google Scholar 

  3. Collier TS, Muddiman DC (2012) Analytical strategies for the global quantification of intact proteins. Amino Acids 43(3):1109–1117

    Article  CAS  PubMed  Google Scholar 

  4. Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A (2014) A draft map of the human proteome. Nature 509(7502):575–581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Tazo Y, Hara A, Onda T, Saegusa M (2014) Bifunctional roles of survivin-DeltaEx3 and survivin-2B for susceptibility to apoptosis in endometrial carcinomas. J Cancer Res Clin Oncol 140:2027–2037

    Article  CAS  Google Scholar 

  6. Arentz G, Weiland F, Oehler MK, Hoffmann P (2015) State of the art of 2D DIGE. Proteomics Clin Appl 9(3–4):277–288

    Article  CAS  PubMed  Google Scholar 

  7. Gorg A, Drews O, Luck C, Weiland F, Weiss W (2009) 2-DE with IPGs. Electrophoresis 30(Suppl 1):S122–S132

    Article  PubMed  Google Scholar 

  8. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1(3):377–396

    Article  CAS  PubMed  Google Scholar 

  9. Shaw J, Rowlinson R, Nickson J, Stone T, Sweet A, Williams K, Tonge R (2003) Evaluation of saturation labelling two-dimensional difference gel electrophoresis fluorescent dyes. Proteomics 3(7):1181–1195

    Article  CAS  PubMed  Google Scholar 

  10. Sitek B, Potthoff S, Schulenborg T, Stegbauer J, Vinke T, Rump LC, Meyer HE, Vonend O, Stuhler K (2006) Novel approaches to analyse glomerular proteins from smallest scale murine and human samples using DIGE saturation labelling. Proteomics 6(15):4337–4345

    Article  CAS  PubMed  Google Scholar 

  11. Arnold GJ, Frohlich T (2012) 2D DIGE saturation labeling for minute sample amounts. Methods Mol Biol 854:89–112

    Article  CAS  PubMed  Google Scholar 

  12. Weiland F, Zammit CM, Reith F, Hoffmann P (2014) High resolution two-dimensional electrophoresis of native proteins. Electrophoresis 35(12–13):1893–1902

    Article  CAS  PubMed  Google Scholar 

  13. Schagger H, von Jagow G (1991) Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem 199(2):223–231

    Article  CAS  PubMed  Google Scholar 

  14. Altenhofer P, Schierhorn A, Fricke B (2006) Agarose isoelectric focusing can improve resolution of membrane proteins in the two-dimensional electrophoresis of bacterial proteins. Electrophoresis 27(20):4096–4111

    Article  CAS  PubMed  Google Scholar 

  15. Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F (2016) Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34. Metallomics 8(11):1204–1216

    Article  CAS  PubMed  Google Scholar 

  16. Heinemeyer J, Scheibe B, Schmitz UK, Braun HP (2009) Blue native DIGE as a tool for comparative analyses of protein complexes. J Proteome 72(3):539–544

    Article  CAS  Google Scholar 

  17. Peters K, Braun HP (2012) Comparative analyses of protein complexes by blue native DIGE. Methods Mol Biol 854:145–154

    Article  CAS  PubMed  Google Scholar 

  18. Reisinger V, Eichacker LA (2012) Native DIGE of fluorescent plant protein complexes. Methods Mol Biol 854:343–353

    Article  CAS  PubMed  Google Scholar 

  19. Gillardon F, Rist W, Kussmaul L, Vogel J, Berg M, Danzer K, Kraut N, Hengerer B (2007) Proteomic and functional alterations in brain mitochondria from Tg2576 mice occur before amyloid plaque deposition. Proteomics 7(4):605–616

    Article  CAS  PubMed  Google Scholar 

  20. Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA (2014) Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mol Cell Proteomics 13(7):1690–1704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Espina V, Edmiston KH, Heiby M, Pierobon M, Sciro M, Merritt B, Banks S, Deng J, VanMeter AJ, Geho DH, Pastore L, Sennesh J, Petricoin EF 3rd, Liotta LA (2008) A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol Cell Proteomics 7(10):1998–2018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Grassl J, Westbrook JA, Robinson A, Boren M, Dunn MJ, Clyne RK (2009) Preserving the yeast proteome from sample degradation. Proteomics 9(20):4616–4626

    Article  CAS  PubMed  Google Scholar 

  23. Ahmed MM, Gardiner KJ (2011) Preserving protein profiles in tissue samples: differing outcomes with and without heat stabilization. J Neurosci Methods 196(1):99–106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kanshin E, Tyers M, Thibault P (2015) Sample collection method bias effects in quantitative Phosphoproteomics. J Proteome Res 14(7):2998–3004

    Article  CAS  PubMed  Google Scholar 

  25. Smejkal GB, Rivas-Morello C, Chang JH, Freeman E, Trachtenberg AJ, Lazarev A, Ivanov AR, Kuo WP (2011) Thermal stabilization of tissues and the preservation of protein phosphorylation states for two-dimensional gel electrophoresis. Electrophoresis 32(16):2206–2215

    Article  CAS  PubMed  Google Scholar 

  26. Acosta-Martin AE, Chwastyniak M, Beseme O, Drobecq H, Amouyel P, Pinet F (2009) Impact of incomplete DNase I treatment on human macrophage proteome analysis. Proteomics Clin Appl 3(10):1236–1246

    Article  CAS  PubMed  Google Scholar 

  27. Righetti PG, Chiari M, Gelfi C (1988) Immobilized pH gradients: effect of salts, added carrier ampholytes and voltage gradients on protein patterns. Electrophoresis 9(2):65–73

    Article  CAS  PubMed  Google Scholar 

  28. Stark GR, Stein WH, Moore S (1960) Reactions of the Cyanate present in aqueous urea with amino acids and proteins. J Biol Chem 235(11):3177–3181

    CAS  Google Scholar 

  29. Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, Mehigh RJ, Cockrill SL, Scott GB, Tammen H, Schulz-Knappe P, Speicher DW, Vitzthum F, Haab BB, Siest G, Chan DW (2005) HUPO plasma proteome project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5(13):3262–3277

    Article  CAS  PubMed  Google Scholar 

  30. Viswanathan S, Unlu M, Minden JS (2006) Two-dimensional difference gel electrophoresis. Nat Protoc 1(3):1351–1358

    Article  CAS  PubMed  Google Scholar 

  31. Mujumdar RB, Ernst LA, Mujumdar SR, Waggoner AS (1989) Cyanine dye labeling reagents containing isothiocyanate groups. Cytometry 10(1):11–19

    Article  CAS  PubMed  Google Scholar 

  32. Karp NA, Lilley KS (2005) Maximising sensitivity for detecting changes in protein expression: experimental design using minimal CyDyes. Proteomics 5(12):3105–3115

    Article  CAS  PubMed  Google Scholar 

  33. Karp NA, Kreil DP, Lilley KS (2004) Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics 4(5):1421–1432

    Article  CAS  PubMed  Google Scholar 

  34. Lilley KS, Friedman DB (2004) All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics 1(4):401–409

    Article  CAS  PubMed  Google Scholar 

  35. Karp NA, McCormick PS, Russell MR, Lilley KS (2007) Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis. Mol Cell Proteomics 6(8):1354–1364

    Article  CAS  PubMed  Google Scholar 

  36. Buncel E, Symons EA (1970) The inherent instability of dimethylformamide-water systems containing hydroxide ion. J Chem Soc D 3:164–165

    Article  Google Scholar 

  37. Wang W, Ackermann D, Mehlich AM, Konig S (2011) Impact of quenching failure of cy dyes in differential gel electrophoresis. PLoS One 6(3):e18098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang W, Ackermann D, Mehlich AM, Konig S (2010) False labelling due to quenching failure of N-hydroxy-succinimide-ester-coupled dyes. Proteomics 10(7):1525–1529

    Article  CAS  PubMed  Google Scholar 

  39. Riederer IM, Herrero RM, Leuba G, Riederer BM (2008) Serial protein labeling with infrared maleimide dyes to identify cysteine modifications. J Proteome 71(2):222–230

    Article  CAS  Google Scholar 

  40. Qu Z, Meng F, Zhou H, Li J, Wang Q, Wei F, Cheng J, Greenlief CM, Lubahn DB, Sun GY, Liu S, Gu Z (2014) NitroDIGE analysis reveals inhibition of protein S-nitrosylation by epigallocatechin gallates in lipopolysaccharide-stimulated microglial cells. J Neuroinflammation 11:17

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Poschmann G, Grzendowski M, Stefanski A, Bruns E, Meyer HE, Stuhler K (2015) Redox proteomics reveal stress responsive proteins linking peroxiredoxin-1 status in glioma to chemosensitivity and oxidative stress. Biochim Biophys Acta 1854(6):624–631

    Article  CAS  PubMed  Google Scholar 

  42. McNamara LE, Kantawong FA, Dalby MJ, Riehle MO, Burchmore R (2011) Preventing and troubleshooting artefacts in saturation labelled fluorescence 2-D difference gel electrophoresis (saturation DiGE). Proteomics 11(24):4610–4621

    Article  CAS  PubMed  Google Scholar 

  43. Bjellqvist B, Ek K, Righetti PG, Gianazza E, Gorg A, Westermeier R, Postel W (1982) Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J Biochem Biophys Methods 6(4):317–339

    Article  CAS  PubMed  Google Scholar 

  44. Righetti PG (1988) Isoelectric focusing as the crow flies. J Biochem Biophys Methods 16(2):99–110

    Article  CAS  PubMed  Google Scholar 

  45. Olsson I, Larsson K, Palmgren R, Bjellqvist B (2002) Organic disulfides as a means to generate streak-free two-dimensional maps with narrow range basic immobilized pH gradient strips as first dimension. Proteomics 2(11):1630–1632

    Article  CAS  PubMed  Google Scholar 

  46. Altland K, Becher P, Rossmann U, Bjellqvist B (1988) Isoelectric focusing of basic proteins: the problem of oxidation of cysteines. Electrophoresis 9(9):474–485

    Article  CAS  PubMed  Google Scholar 

  47. Görg A, Klaus A, Lück C, Weiland F, Weiss W (2007) Two-dimensional electrophoresis with immobilized pH gradients for proteome analysis: a laboratory manual. Technische Universität München, Freising-Weihenstephan, München

    Google Scholar 

  48. Görg A, Postel W, Weser J, Günther S, Strahler JR, Hanash SM, Somerlot L (1987) Elimination of point streaking on silver stained two-dimensional gels by addition of iodoacetamide to the equilibration buffer. Electrophoresis 8(2):122–124

    Article  Google Scholar 

  49. Westermeier R, Görg A (2011) Two-dimensional electrophoresis in proteomics. In: Protein purification. John Wiley & Sons, Inc., Hoboken, pp 411–439

    Chapter  Google Scholar 

  50. Morris JS, Clark BN, Wei W, Gutstein HB (2010) Evaluating the performance of new approaches to spot quantification and differential expression in 2-dimensional gel electrophoresis studies. J Proteome Res 9(1):595–604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Morris JS, Clark BN, Gutstein HB (2008) Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data. Bioinformatics 24(4):529–536

    Article  CAS  PubMed  Google Scholar 

  52. Sellers KF, Miecznikowski J, Viswanathan S, Minden JS, Eddy WF (2007) Lights, camera, action! Systematic variation in 2-D difference gel electrophoresis images. Electrophoresis 28(18):3324–3332

    Article  CAS  PubMed  Google Scholar 

  53. Jung K, Gannoun A, Sitek B, Meyer HE, Stühler K, Urfer W (2005) Analysis of dynamic protein expression data. RevStat: Statist J 3(2):99–111

    Google Scholar 

  54. Dowsey AW, Dunn MJ, Yang GZ (2008) Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline. Bioinformatics 24(7):950–957

    Article  CAS  PubMed  Google Scholar 

  55. Dowsey AW, English J, Pennington K, Cotter D, Stuehler K, Marcus K, Meyer HE, Dunn MJ, Yang GZ (2006) Examination of 2-DE in the human proteome organisation brain proteome project pilot studies with the new RAIN gel matching technique. Proteomics 6(18):5030–5047

    Article  CAS  PubMed  Google Scholar 

  56. Veeser S, Dunn MJ, Yang GZ (2001) Multiresolution image registration for two-dimensional gel electrophoresis. Proteomics 1(7):856–870

    Article  CAS  PubMed  Google Scholar 

  57. Clark BN, Gutstein HB (2008) The myth of automated, high-throughput two-dimensional gel analysis. Proteomics 8(6):1197–1203

    Article  CAS  PubMed  Google Scholar 

  58. Keeping AJ, Collins RA (2011) Data variance and statistical significance in 2D-gel electrophoresis and DIGE experiments: comparison of the effects of normalization methods. J Proteome Res 10(3):1353–1360

    Article  CAS  PubMed  Google Scholar 

  59. Pursiheimo A, Vehmas AP, Afzal S, Suomi T, Chand T, Strauss L, Poutanen M, Rokka A, Corthals GL, Elo LL (2015) Optimization of statistical methods impact on quantitative proteomics data. J Proteome Res 14(10):4118–4126

    Article  CAS  PubMed  Google Scholar 

  60. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100(16):9440–9445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Storey JD (2002) A direct approach to false discovery rates. J R Statist SocB 64(3):479–498

    Article  Google Scholar 

  62. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist SocB 57:289–300

    Google Scholar 

  63. Laeremans A, Van de Plas B, Clerens S, Van den Bergh G, Arckens L, Hu TT (2013) Protein expression dynamics during postnatal mouse brain development. J Exp Neurosci 7:61–74

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. Pinaud R, Osorio C, Alzate O, Jarvis ED (2008) Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics. Eur J Neurosci 27(6):1409–1422

    Article  PubMed  PubMed Central  Google Scholar 

  65. Simor A, Gyorffy BA, Gulyassy P, Volgyi K, Toth V, Todorov MI, Kis V, Borhegyi Z, Szabo Z, Janaky T, Drahos L, Juhasz G, Kekesi KA (2017) The short- and long-term proteomic effects of sleep deprivation on the cortical and thalamic synapses. Mol Cell Neurosci 79:64–80

    Article  CAS  PubMed  Google Scholar 

  66. Volgyi K, Udvari EB, Szabo ER, Gyorffy BA, Hunyadi-Gulyas E, Medzihradszky K, Juhasz G, Kekesi KA, Dobolyi A (2017) Maternal alterations in the proteome of the medial prefrontal cortex in rat. J Proteome 153:65–77

    Article  CAS  Google Scholar 

  67. Udvari EB, Volgyi K, Gulyassy P, Dimen D, Kis V, Barna J, Szabo ER, Lubec G, Juhasz G, Kekesi KA, Dobolyi A (2017) Synaptic proteome changes in the hypothalamus of mother rats. J Proteome 159:54–66

    Article  CAS  Google Scholar 

  68. Laskowska-Macios K, Nys J, Hu TT, Zapasnik M, Van der Perren A, Kossut M, Burnat K, Arckens L (2015) Binocular pattern deprivation interferes with the expression of proteins involved in primary visual cortex maturation in the cat. Mol Brain 8:48

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  69. Osorio C, Sullivan PM, He DN, Mace BE, Ervin JF, Strittmatter WJ, Alzate O (2007) Mortalin is regulated by APOE in hippocampus of AD patients and by human APOE in TR mice. Neurobiol Aging 28(12):1853–1862

    Article  CAS  PubMed  Google Scholar 

  70. Voos W, Rottgers K (2002) Molecular chaperones as essential mediators of mitochondrial biogenesis. Biochim Biophys Acta 1592(1):51–62

    Article  CAS  PubMed  Google Scholar 

  71. Volgyi K, Haden K, Kis V, Gulyassy P, Badics K, Gyorffy BA, Simor A, Szabo Z, Janaky T, Drahos L, Dobolyi A, Penke B, Juhasz G, Kekesi KA (2017) Mitochondrial proteome changes correlating with beta-amyloid accumulation. Mol Neurobiol 54(3):2060–2078

    Article  CAS  PubMed  Google Scholar 

  72. Laramee ME, Smolders K, Hu TT, Bronchti G, Boire D, Arckens L (2016) Congenital Anophthalmia and binocular neonatal Enucleation differently affect the proteome of primary and secondary visual cortices in mice. PLoS One 11(7):e0159320

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Gellen B, Volgyi K, Gyorffy BA, Darula Z, Hunyadi-Gulyas E, Baracskay P, Czurko A, Hernadi I, Juhasz G, Dobolyi A, Kekesi KA (2017) Proteomic investigation of the prefrontal cortex in the rat clomipramine model of depression. J Proteome 153:53–64

    Article  CAS  Google Scholar 

  74. Catherman AD, Skinner OS, Kelleher NL (2014) Top down proteomics: facts and perspectives. Biochem Biophys Res Commun 445(4):683–693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The author wants to thank Maithili Shroff for proof-reading the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Florian Weiland .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Weiland, F. (2019). 2D-DIGE as a Tool in Neuroproteomics. In: Li, K. (eds) Neuroproteomics. Neuromethods, vol 146. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9662-9_13

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9662-9_13

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9661-2

  • Online ISBN: 978-1-4939-9662-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics