Comparative 2D DIGE Analysis of the Depleted Serum Proteome for Biomarker Discovery

  • Megan Penno
  • Matthias Ernst
  • Peter HoffmannEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 854)


Serum is unarguably the most used diagnostic fluid. As it circulates throughout the body, leakage peptides/proteins from damaged and dying cells, host-response proteins including inflammatory mediators, and aberrant secretions from tumors and diseased tissues are released into serum, potentially providing a rich source of disease biomarkers. Here, a method for extending access to the serum proteome by removing highly abundant proteins prior to comparative two-dimensional difference gel electrophoresis (2D DIGE) and subsequent protein digestion for identification by mass spectrometry is described.

Key words

Biomarkers Serum Depletion Multiple affinity removal system Tryptic digestion 


  1. 1.
    Anderson NL, Anderson NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 1(11):845–67.PubMedCrossRefGoogle Scholar
  2. 2.
    Jacobs JM, Adkins JN, Qian WJ, Liu T, Shen Y, Camp DG 2nd, Smith RD (2005) Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res. 4(4):1073–85PubMedCrossRefGoogle Scholar
  3. 3.
    Anderson L (2005) Candidate-based proteomics in the search for biomarkers of cardiovascular disease. J Physiol. 563(Pt 1):23–60.PubMedGoogle Scholar
  4. 4.
    Thadikkaran L, Siegenthaler MA, Crettaz D, Queloz PA, Schneider P, Tissot JD (2005) Recent advances in blood-related proteomics. Proteomics. 5(12):3019–34.PubMedCrossRefGoogle Scholar
  5. 5.
    Lollo BA, Harvey S, Liao J, Stevens AC, Wagenknecht R, Sayen R, Whaley J, Sajjadi FG (1999) Improved two-dimensional gel electrophoresis representation of serum proteins by using ProtoClear. Electrophoresis. 20(4–5):854–9.PubMedCrossRefGoogle Scholar
  6. 6.
    Sato AK, Sexton DJ, Morganelli LA, Cohen EH, Wu QL, Conley GP, Streltsova Z, Lee SW, Devlin M, DeOliveira DB, Enright J, Kent RB, Wescott CR, Ransohoff TC, Ley AC, Ladner RC (2002) Development of mammalian serum albumin affinity purification media by peptide phage display. Biotechnol Prog. 18(2):182–92.PubMedCrossRefGoogle Scholar
  7. 7.
    Boschetti E, Righetti PG (2008) The ProteoMiner in the proteomic arena: a non-depleting tool for discovering low-abundance species. J Proteomics. 71(3):255–64.PubMedCrossRefGoogle Scholar
  8. 8.
    Gong Y, Li X, Yang B, Ying W, Li D, Zhang Y, Dai S, Cai Y, Wang J, He F, Qian X (2006) Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res. 5(6):1379–87.PubMedCrossRefGoogle Scholar
  9. 9.
    Rai AJ, Vitzthum F (2006) Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics. Expert Rev Proteomics. 3(4):409–26.PubMedCrossRefGoogle Scholar
  10. 10.
    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.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Adelaide Proteomics CentreUniversity of AdelaideAdelaideAustralia
  2. 2.Ludwig Centre for Cancer ResearchParkvilleAustralia

Personalised recommendations