Online Monitoring of Immunoaffinity-based Depletion of High-abundance Blood Proteins by UV Spectrophotometry Using Enhanced Green Fluorescence Protein and FITC-labeled Human Serum Albumin

Overview

Journal Proteome Sci

Publisher Biomed Central

Date 2010 Dec 3

PMID 21122139

Authors

Kyunggon Kim

Jiyoung Yu

Hophil Min

Hyunsoo Kim

Byungwook Kim

Hyeong Gon Yu

YoungSoo Kim

Affiliations

Soon will be listed here.

Abstract

Background: The removal of high-abundance proteins from plasma is an efficient approach to investigating flow-through proteins for biomarker discovery studies. Most depletion methods are based on multiple immunoaffinity methods available commercially including LC columns and spin columns. Despite its usefulness, high-abundance depletion has an intrinsic problem, the sponge effect, which should be assessed during depletion experiments. Concurrently, the yield of depletion of high-abundance proteins must be monitored during the use of the depletion column. To date, there is no reasonable technique for measuring the recovery of flow-through proteins after depletion and assessing the capacity for capture of high-abundance proteins.

Results: In this study, we developed a method of measuring recovery yields of a multiple affinity removal system column easily and rapidly using enhanced green fluorescence protein as an indicator of flow-through proteins. Also, we monitored the capture efficiency through depletion of a high-abundance protein, albumin labeled with fluorescein isothiocyanate.

Conclusion: This simple method can be applied easily to common high-abundance protein depletion methods, effectively reducing experimental variations in biomarker discovery studies.

References

Petricoin E, Liotta L . SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer. Curr Opin Biotechnol. 2004; 15(1):24-30. DOI: 10.1016/j.copbio.2004.01.005. View

Zolotarjova N, Martosella J, Nicol G, Bailey J, Boyes B, Barrett W . Differences among techniques for high-abundant protein depletion. Proteomics. 2005; 5(13):3304-13. DOI: 10.1002/pmic.200402021. View

Wang Y, Cheung Y, Yang Z, Chiu J, Che C, He Q . Proteomic approach to study the cytotoxicity of dioscin (saponin). Proteomics. 2006; 6(8):2422-32. DOI: 10.1002/pmic.200500595. View

Lei T, He Q, Wang Y, Si L, Chiu J . Heparin chromatography to deplete high-abundance proteins for serum proteomics. Clin Chim Acta. 2007; 388(1-2):173-8. DOI: 10.1016/j.cca.2007.10.034. View

Huang L, Harvie G, Feitelson J, Gramatikoff K, Herold D, Allen D . Immunoaffinity separation of plasma proteins by IgY microbeads: meeting the needs of proteomic sample preparation and analysis. Proteomics. 2005; 5(13):3314-28. DOI: 10.1002/pmic.200401277. View

Brand J, Haslberger T, Zolg W, Pestlin G, Palme S . Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column. Proteomics. 2006; 6(11):3236-42. DOI: 10.1002/pmic.200500864. View

Pieper R, Su Q, Gatlin C, Huang S, Anderson N, Steiner S . Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome. Proteomics. 2003; 3(4):422-32. DOI: 10.1002/pmic.200390057. View

Sitnikov D, Chan D, Thibaudeau E, Pinard M, Hunter J . Protein depletion from blood plasma using a volatile buffer. J Chromatogr B Analyt Technol Biomed Life Sci. 2006; 832(1):41-6. DOI: 10.1016/j.jchromb.2005.12.013. View

Bjorhall K, Miliotis T, Davidsson P . Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics. 2004; 5(1):307-17. DOI: 10.1002/pmic.200400900. View

10.

Zhang G, Gurtu V, Kain S . An enhanced green fluorescent protein allows sensitive detection of gene transfer in mammalian cells. Biochem Biophys Res Commun. 1996; 227(3):707-11. DOI: 10.1006/bbrc.1996.1573. View

11.

Lelong C, Chevallet M, Luche S, Rabilloud T . Silver staining of proteins in 2DE gels. Methods Mol Biol. 2009; 519:339-50. DOI: 10.1007/978-1-59745-281-6_21. View

12.

Ordog R . PyDeT, a PyMOL plug-in for visualizing geometric concepts around proteins. Bioinformation. 2008; 2(8):346-7. PMC: 2478735. DOI: 10.6026/97320630002346. View

13.

Bellei E, Bergamini S, Monari E, Fantoni L, Cuoghi A, Ozben T . High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins. Amino Acids. 2010; 40(1):145-56. DOI: 10.1007/s00726-010-0628-x. View

14.

Yang T, Cheng L, Kain S . Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. Nucleic Acids Res. 1996; 24(22):4592-3. PMC: 146266. DOI: 10.1093/nar/24.22.4592. View

15.

Freeman W, Lull M, Guilford M, Vrana K . Depletion of abundant proteins from non-human primate serum for biomarker studies. Proteomics. 2006; 6(10):3109-13. DOI: 10.1002/pmic.200500717. View

16.

Zhou M, Lucas D, Chan K, Issaq H, Petricoin 3rd E, Liotta L . An investigation into the human serum "interactome". Electrophoresis. 2004; 25(9):1289-98. DOI: 10.1002/elps.200405866. View

17.

Yocum A, Yu K, Oe T, Blair I . Effect of immunoaffinity depletion of human serum during proteomic investigations. J Proteome Res. 2005; 4(5):1722-31. DOI: 10.1021/pr0501721. View

18.

Echan L, Tang H, Ali-Khan N, Lee K, Speicher D . Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma. Proteomics. 2005; 5(13):3292-303. DOI: 10.1002/pmic.200401228. View

19.

Park J, Kwon H, Kang Y, Kim Y . Proteomic analysis of O-GlcNAc modifications derived from streptozotocin and glucosamine induced beta-cell apoptosis. J Biochem Mol Biol. 2007; 40(6):1058-68. DOI: 10.5483/bmbrep.2007.40.6.1058. View

20.

Tu C, Rudnick P, Martinez M, Cheek K, Stein S, Slebos R . Depletion of abundant plasma proteins and limitations of plasma proteomics. J Proteome Res. 2010; 9(10):4982-91. PMC: 2948641. DOI: 10.1021/pr100646w. View