Abstract
This chapter will focus on upstream immunodepletion of high abundant proteins from plasma samples and subsequent analysis by difference gel electrophoresis (DIGE). The abundances of proteins in biofluid proteomes, such as serum, plasma, saliva, and bronchoalveolar lavage fluid (BALF), can exceed 10 orders of magnitude. This substantial dynamic range is problematic for the detection of medium and low abundance proteins by DIGE analysis. To increase the detection, quantification, and identification of medium-low abundant proteins, the targeted depletion of known abundant proteins with antibody columns has been successfully employed. From the literature, it is clear that the performance of abundant protein depletion with immunodepletion columns has been successful in broadening the coverage of the biofluid proteome and facilitating the identification of disease-specific biomarkers. The task for a successful biomarker strategy involves the combination of a reproducible and robust fractionation method, coupled with a highly accurate quantitative method, a task that is exemplified by combining both immunodepletion and DIGE together to discover significant proteins associated with the disease phenotype.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Huang Z, Ma L, Huang C, Li Q, Nice EC (2016) Proteomic profiling of human plasma for cancer biomarker discovery. Proteomics. doi:10.1002/pmic.201600240
Dowling P, Meleady P, Henry M, Clynes M (2010) Recent advances in clinical proteomics using mass spectrometry. Bioanalysis 2(9):1609–1615. doi:10.4155/bio.10.69
Zhang Q, Faca V, Hanash S (2011) Mining the plasma proteome for disease applications across seven logs of protein abundance. J Proteome Res 10(1):46–50. doi:10.1021/pr101052y
Anderson NL, Anderson NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1(11):845–867
Surinova S, Schiess R, Hüttenhain R, Cerciello F, Wollscheid B, Aebersold R (2011) On the development of plasma protein biomarkers. J Proteome Res 10(1):5–16. doi:10.1021/pr1008515
Teng PN, Bateman NW, Hood BL, Conrads TP (2010) Advances in proximal fluid proteomics for disease biomarker discovery. J Proteome Res 9(12):6091–6100. doi:10.1021/pr100904q
Kim MR, Kim CW (2007) Human blood plasma preparation for two-dimensional gel electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 849(1–2):203–210. doi:10.1016/j.jchromb.2006.11.046
Polaskova V, Kapur A, Khan A, Molloy MP, Baker MS (2010) High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis 31(3):471–482. doi:10.1002/elps.200900286
Gundry RL, White MY, Nogee J, Tchernyshyov I, Van Eyk JE (2009) Assessment of albumin removal from an immunoaffinity spin column: critical implications for proteomic examination of the albuminome and albumin-depleted samples. Proteomics 9(7):2021–2028. doi:10.1002/pmic.200800686
Fernández-Costa C, Calamia V, Fernández-Puente P, Capelo-Martínez JL, Ruiz-Romero C, Blanco FJ (2012) Sequential depletion of human serum for the search of osteoarthritis biomarkers. Proteome Sci 10(1):55. doi:10.1186/1477-5956-10-55
Timms JF, Arslan-Low E, Kabir M, Worthington J, Camuzeaux S, Sinclair J, Szaub J, Afrough B, Podust VN, Fourkala EO, Cubizolles M, Kronenberg F, Fung ET, Gentry-Maharaj A, Menon U, Jacobs I (2014) Discovery of serum biomarkers of ovarian cancer using complementary proteomic profiling strategies. Proteomics Clin Appl 8(11–12):982–993. doi:10.1002/prca.201400063
Pieper R, Su Q, Gatlin CL, Huang ST, Anderson NL, Steiner S (2003) Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3(4):422–432. doi:10.1002/pmic.200390057
Gourin CG, Zhi W, Adam BL (2009) Proteomic identification of serum biomarkers for head and neck cancer surveillance. Laryngoscope 119(7):1291–1302. doi:10.1002/lary.20279
Rajpal R, Dowling P, Meiller J, Clarke C, Murphy WG, O’Connor R, Kell M, Mitsiades C, Richardson P, Anderson KC, Clynes M, O'Gorman P (2011) A novel panel of protein biomarkers for predicting response to thalidomide-based therapy in newly diagnosed multiple myeloma patients. Proteomics 11(8):1391–1402. doi:10.1002/pmic.201000471
Fahiminiya S, Roche S, Gérard N (2012) Improvement of 2D-PAGE resolution of human, porcine and canine follicular fluid: comparison of two immunodepletion columns. Reprod Domest Anim 47(5):e67–e70. doi:10.1111/j.1439-0531.2011.01939.x
Patel BB, Barrero CA, Braverman A, Kim PD, Jones KA, Chen DE, Bowler RP, Merali S, Kelsen SG, Yeung AT (2012) Assessment of two immunodepletion methods: off-target effects and variations in immunodepletion efficiency may confound plasma proteomics. J Proteome Res 11(12):5947–5958. doi:10.1021/pr300686k
Corrigan L, Jefferies C, Clive Lee T, Daly J (2011) Evaluation and optimization of IgY spin column technology in the depletion of abundant proteins from human serum. Proteomics 11(16):3415–3419. doi:10.1002/pmic.201000587
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Dowling, P., Ohlendieck, K. (2018). DIGE Analysis of Immunodepleted Plasma. In: Ohlendieck, K. (eds) Difference Gel Electrophoresis. Methods in Molecular Biology, vol 1664. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7268-5_19
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7268-5_19
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7267-8
Online ISBN: 978-1-4939-7268-5
eBook Packages: Springer Protocols