Abstract
Protein biomarker discovery in blood plasma and serum is severely hampered by the vast dynamic range of the proteome. With protein concentrations spanning 12 orders of magnitude, conventional mass spectrometric analysis allows for detection of only a few low-abundance proteins. Prior depletion of high-abundant proteins from the sample can increase analytical depth considerably and has become a widely used practice. We describe in detail an affinity depletion method that selectively removes 14 of the most abundant proteins in plasma and serum.
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
References
Zhou M, Lucas DA, Chan KC et al (2004) An investigation into the human serum “interactome”. Electrophoresis 25:1289–1298
Rai AJ, Gelfand CA, Haywood BC et al (2005) HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5:3262–3277
Burtis CA, Ashwood ER (2001) Tietz fundamentals of clinical chemistry, 5th edn. Saunders Company, Philadelphia, PA
Wrotnowski C (1998) The future of plasma proteins. Gen Eng News 18:14
Anderson NL, Anderson NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1:845–867
Tirumalai RS, Chan KC, Prieto DA, Issaq HJ, Conrads TP, Veenstra TD (2003) Characterization of the low molecular weight human serum proteome. Mol Cell Proteomics 2:1096–1103
Hoffman SA, Joo WA, Echan LA, Speicher DW (2007) Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J Chromatogr B Analyt Technol Biomed Life Sci 849:43–52
Annesley TM (2003) Ion suppression in mass spectrometry. Clin Chem 49:1041–1044
Faca V, Pitteri SJ, Newcomb L et al (2007) Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res 6:3558–3565
Smith MPW, Wood SL, Zougman A et al (2011) A systematic analysis of the effects of increasing degrees of serum immunodepletion in terms of depth of coverage and other key aspects in top-down and bottom-up proteomic analyses. Proteomics 11:2222–2235
Tang H-Y, Beer LA, Barnhart KT, Speicher DW (2011) Rapid verification of candidate serological biomarkers using gel-based, label-free multiple reaction monitoring. J Proteome Res 10:4005–4017
Zhao L, Liu Y, Sun X, Peng K, Ding Y (2011) Serum proteome analysis for profiling protein markers associated with lymph node metastasis in colorectal carcinoma. J Comp Pathol 144:187–194
Liao Q, Zhao L, Chen X, Deng Y, Ding Y (2008) Serum proteome analysis for profiling protein markers associated with carcinogenesis and lymph node metastasis in nasopharyngeal carcinoma. Clin Exp Metastasis 25:465–476
Hamrita B, Chahed K, Trimeche M et al (2009) Proteomics-based identification of alpha1-antitrypsin and haptoglobin precursors as novel serum markers in infiltrating ductal breast carcinomas. Clin Chim Acta 404: 111–118
Kaur P, Reis MD, Couchman GR, Forjuoh SN, Greene JF, Asea A (2010) SERPINE 1 links obesity and diabetes: a pilot study. J Proteomics Bioinform 3:191–199
Fratantoni SA, Piersma SR, Jimenez CR (2010) Comparison of the performance of two affinity depletion spin filters for quantitative proteomics of CSF: evaluation of sensitivity and reproducibility of CSF analysis using GeLC-MS/MS and spectral counting. Proteomics Clin Appl 4:613–617
Siegmund R, Kiehntopf M, Deufel T (2009) Evaluation of two different albumin depletion strategies for improved analysis of human CSF by SELDI-TOF-MS. Clin Biochem 42:1136–1143
Zuberovic A, Hanrieder J, Hellman U, Bergquist J, Wetterhall M (2008) Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples. Eur J Mass Spectrom 14:249–260
Thouvenot E, Urbach S, Dantec C et al (2008) Enhanced detection of CNS cell secretome in plasma protein-depleted cerebrospinal fluid. J Proteome Res 7:4409–4421
Sigdel TK, Lau K, Schilling J, Sarwal M (2008) Optimizing protein recovery for urinary proteomics, a tool to monitor renal transplantation. Clin Transplant 22:617–623
Zolotarjova N, Martosella J, Nicol G, Bailey J, Boyes BE, Barrett WC (2005) Differences among techniques for high-abundant protein depletion. Proteomics 5:3304–3313
Koutroukides TA, Guest PC, Leweke FM et al (2011) Characterization of the human serum depletome by label-free shotgun proteomics. J Sep Sci 34:1621–1626
Fania C, Vasso M, Torretta E et al (2011) Setup for human sera MALDI profiling: the case of rhEPO treatment. Electrophoresis 32:1715–1727
Martosella J, Zolotarjova N, Liu H, Nicol G, Boyes BE (2005) Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins. J Proteome Res 4:1522–1537
Björhall K, Miliotis T, Davidsson P (2005) Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 5:307–317
Acknowledgments
This work was supported by the Stanley Medical Research Institute (SMRI, USA), Psynova Neurotech (UK), and European Union FP7 SchizDX research program (grant reference 223427).
JAJJ and DMS declare no conflict of interest. PCG and SB are consultants for Myriad-RBM although this does interfere with Springer Science policies with regards to sharing of data or materials.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Jaros, J.A.J., Guest, P.C., Bahn, S., Martins-de-Souza, D. (2013). Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis. In: Zhou, M., Veenstra, T. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1002. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-360-2_1
Download citation
DOI: https://doi.org/10.1007/978-1-62703-360-2_1
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-359-6
Online ISBN: 978-1-62703-360-2
eBook Packages: Springer Protocols