Avoiding nonspecific interactions in studies of the plasma proteome: Practical solutions to prevention of nonspecific interactions for label-free detection of low-abundance plasma proteins

Journal of Proteome Research

Volumn 8, Issue 11, 2009, Pages 5103-5110

  Richens, Joanna L ^a   Lunt, Elizabeth A M ^a   Sanger, Daniel ^a   McKenzie, Graeme ^a   O'Shea, Paul ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Albumin; Blood; Cytokine; Microarray; Plasma proteome; Thiocyanate

Indexed keywords

ALBUMIN; PLASMA PROTEIN; PROTEOME;

ANTIGEN ANTIBODY REACTION; ARTICLE; CONTROLLED STUDY; HUMAN; HYDROPHOBICITY; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

BLOOD PROTEINS; ERYTHROCYTES; HUMANS; PLASMA; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING; PROTEOME; SENSITIVITY AND SPECIFICITY; THIOCYANATES;

EID: 70449354972     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900487y     Document Type: Article

References (31)

1. Drake, R. R.; Cazares, L.; Semmes, O. J. Mining the low molecular weight proteome of blood. Proteomics Clin. Appl. 2007, 1 (8), 758-768.
2. Crawford, E. D.; Abrahamsson, P. A. PSA-based screening for prostate cancer: how does it compare with other cancer screening tests. Eur. Urol. 2008, 54 (2), 262-273.
3. Pal, S. K.; Pegram, M. HER2 targeted therapy in breast cancer..beyond Herceptin. Rev. Endocr. Metab. Disord. 2007, 8 (3), 269-277. (Pubitemid 47524873)
4. Rubin, I.; Yarden, Y. The basic biology of HER2. Ann. Oncol. 2001, 12, S3-8.
5. Yarden, Y. Biology of HER2 and its importance in breast cancer. Oncology 2001, 61, 1-13. (Pubitemid 33033419)
6. Gong, Y.; Li, X.; Yang, B.; Ying, W.; Li, D.; Zhang, Y.; Dai, S.; Cai, Y.; Wang, J.; He, F.; Qian, X. Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J. Proteome Res. 2006, 5 (6), 1379-1387. (Pubitemid 43865808)
7. Fountoulakis, M.; Juranville, J. F.; Jiang, L.; Avila, D.; Roder, D.; Jakob, P.; Berndt, P.; Evers, S.; Langen, H. Depletion of the highabundance plasma proteins. Amino Acids 2004, 27 (3-4), 249-259.
8. Merrell, K.; Southwick, K.; Graves, S. W.; Esplin, M. S.; Lewis, N. E.; Thulin, C. D. Analysis of low-abundance, low-molecular-weight serum proteins using mass spectrometry. J. Biomol. Tech. 2004, 15 (4), 238-248.
9. Anderson, N. L.; Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1 (11), 845-867.
10. Prinsen, B. H.; de Sain-van der Velden, M. G. Albumin turnover: experimental approach and its application in health and renal diseases. Clin. Chim. Acta 2004, 347 (1-2), 1-14.
11. Rengarajan, K.; de Smet, M. D.; Wiggert, B. Removal of albumin from multiple human serum samples. BioTechniques 1996, 20 (1), 30-32. (Pubitemid 26025522)
12. Seferovic, M. D.; Krughkov, V.; Pinto, D.; Han, V. K.; Gupta, M. B. Quantitative 2-D gel electrophoresis-based expression proteomics of albumin and IgG immunodepleted plasma. J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2008, 865 (1-2), 147-152.
13. Peters, T., Jr. All About Albumin: Biochemistry, Genetics, and Medical Applications; Academic Press: San Diego, CA, 1995; pp 9-75.
14. Greenough, C.; Jenkins, R. E.; Kitteringham, N. R.; Pirmohamed, M.; Park, B. K.; Pennington, S. R. A method for the rapid depletion of albumin and immunoglobulin from human plasma. Proteomics 2004, 4 (10), 3107-3111. (Pubitemid 39372392)
15. Rothemund, D. L.; Locke, V. L.; Liew, A.; Thomas, T. M.; Wasinger, V.; Rylatt, D. B. Depletion of the highly abundant protein albumin from human plasma using the Gradiflow. Proteomics 2003, 3 (3), 279-287.
16. Linke, T.; Doraiswamy, S.; Harrison, E. H. Rat plasma proteomics: effects of abundant protein depletion on proteomic analysis. J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2007, 849 (1-2), 273-281.
17. Vestergaard, M.; Tamiya, E. A rapid sample pretreatment protocol: improved sensitivity in the detection of a low-abundant serum biomarker for prostate cancer. Anal. Sci. 2007, 23 (12), 1443-1446.
18. Bjorhall, K.; Miliotis, T.; Davidsson, P. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 2005, 5 (1), 307-317. (Pubitemid 40189661)
19. Granger, J.; Siddiqui, J.; Copeland, S.; Remick, D. Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics 2005, 5 (18), 4713-4718. (Pubitemid 43016893)
20. Ahmed, N.; Barker, G.; Oliva, K.; Garfin, D.; Talmadge, K.; Georgiou, H.; Quinn, M.; Rice, G. An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum. Proteomics 2003, 3 (10), 1980-1987. (Pubitemid 37305892)
21. Mehta, A. I.; Ross, S.; Lowenthal, M. S.; Fusaro, V.; Fishman, D. A.; Petricoin, E. F., III; Liotta, L. A. Biomarker amplification by serum carrier protein binding. Dis. Markers 2003, 19 (1), 1-10.
22. Qin, S.; Ferdinand, A. S.; Richie, J. P.; O'Leary, M. P.; Mok, S. C.; Liu, B. C. Chromatofocusing fractionation and two-dimensional difference gel electrophoresis for low abundance serum proteins. Proteomics 2005, 5 (12), 3183-3192.
23. Aresta, A.; Calvano, C. D.; Palmisano, F.; Zambonin, C. G.; Monaco, A.; Tommasi, S.; Pilato, B.; Paradiso, A. Impact of sample preparation in peptide/protein profiling in human serum by MALDI-TOF mass spectrometry. J. Pharm. Biomed. Anal. 2008, 46 (1), 157-164. (Pubitemid 350216342)
24. Dekker, L. J.; Bosman, J.; Burgers, P. C.; van Rijswijk, A.; Freije, R.; Luider, T.; Bischoff, R. Depletion of high-abundance proteins from serum by immunoaffinity chromatography: a MALDI-FT-MS study. J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2007, 847 (1), 65-69. (Pubitemid 46216197)
25. Richens, J. L.; Urbanowicz, R. A.; Lunt, E. A.; Metcalf, R.; Corne, J.; Fairclough, L.; O'Shea, P. Systems biology coupled with label-free high-throughput detection as a novel approach for diagnosis of chronic obstructive pulmonary disease. Resp. Res. 2009, 10, 29-46.
26. Wall, J.; Ayoub, F.; O'Shea, P. Interactions of macromolecules with the mammalian cell surface. J. Cell Sci. 1995, 108, 2673-2682.
27. Mayer, L. D.; Hope, M. J.; Cullis, P. R. Vesicles of variable sizes produced by a rapid extrusion procedure. Biochim. Biophys. Acta 1986, 858 (1), 161-168.
28. Wall, J.; Ayoub, F.; O'Shea, P. A study of the interactions of an immunoglobulin light chain with artificial and B-lymphocyte membranes. Front. Biosci. 1996, 1, a46-58.
29. Yu, X.; Xu, D.; Cheng, Q. Label-free detection methods for protein microarrays. Proteomics 2006, 6 (20), 5493-5503 (Pubitemid 44683217)
30. Martich, G. D.; Danner, R. L.; Ceska, M.; Suffredini, A. F. Detection of interleukin 8 and tumor necrosis factor in normal humans after intravenous endotoxin: the effect of antiinflammatory agents. J. Exp. Med. 1991, 173 (4), 1021-1024.
31. O'Shea, P. Membrane Potentials; Measurement, Occurrence & Roles in Cellular Function. In Bioelectrochemistry of Membranes; Walz, D. , et al., Eds.; Birkhauser Verlag: Switzerland, 2004; pp 23-59.