Targeting interferon alpha subtypes in serum: A comparison of analytical approaches to the detection and quantitation of proteins in complex biological matrices

Journal of Proteome Research

Volumn 8, Issue 6, 2009, Pages 3132-3140

  Izrael Tomasevic, Anita ^a   Phu, Lilian ^a   Phung, Qui T ^a   Lill, Jennie R ^a   Arnott, David ^a,b  

^a GENENTECH INC   (United States)

^b MS 63 ^*  (United States)

Author keywords

Accurate mass tag; Interferon alpha; Isotope dilution; LC MSn; Mass spectrometry; Quantitation; Serum

Indexed keywords

ALPHA INTERFERON;

ARTICLE; ISOTOPE DILUTION ASSAY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN ISOLATION; QUANTITATIVE ANALYSIS; SERUM;

CALIBRATION; CHROMATOGRAPHY, ION EXCHANGE; HUMANS; INTERFERON-ALPHA; ISOTOPE LABELING; LINEAR MODELS; MASS SPECTROMETRY; SENSITIVITY AND SPECIFICITY;

EID: 67049172101     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900076q     Document Type: Article

References (29)

1. Anderson, N. L.; Anderson, N. G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 2002, 1 (11), 845-867
2. Bienvenu, J. A.; Monneret, G.; Gutowski, M. C.; Fabien, N. Cytokine assays in human sera and tissues. Toxicology 1998, 129 (1), 55-61. (Pubitemid 29084431)
3. Diaz, M. O.; Bohlander, S.; Allen, G. Nomenclature of the human interferon genes. J. Interferon Cytokine Res. 1996, 16 (2), 179-180 (Pubitemid 26074173)
4. Hooks, J. J.; Moutsopoulos, H. M.; Geis, S. A.; Stahl, N. I.; Decker, J. L.; Notkins, A. L. Immune interferon in the circulation of patients with autoimmune disease. N. Engl. J. Med. 1979, 301 (1), 5-8. (Pubitemid 9226519)
5. Stewart, T. A. Neutralizing interferon alpha as a therapeutic approach to autoimmune diseases. Cytokine Growth Factor Rev. 2003, 14 (2), 139-154 (Pubitemid 36389527)
6. Fitzgerald, S. P.; McConnell, R. I.; Huxley, A. Simultaneous analysis of circulating human cytokines using a high-sensitivity cytokine biochip array. J. Proteome Res. 2008, 7 (1), 450-455 (Pubitemid 351171159)
7. Wadhwa, M.; Thorpe, R. Cytokine immunoassays: recommendations for standardisation, calibration and validation. J. Immunol. Methods 1998, 219 (1-2), 1-5. (Pubitemid 28513148)
8. Lescuyer, P.; Hochstrasser, D.; Rabilloud, T. How shall we use the proteomics toolbox for biomarker discovery. J. Proteome Res. 2007, 6 (9), 3371-3376 (Pubitemid 47522726)
9. Good, D. M.; Thongboonkerd, V.; Novak, J.; Bascands, J. L.; Schanstra, J. P.; Coon, J. J.; Dominiczak, A.; Mischak, H. Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future. J. Proteome Res. 2007, 6 (12), 4549-4555
10. Hu, S.; Loo, J. A.; Wong, D. T. Human body fluid proteome analysis. Proteomics 2006, 6 (23), 6326-6353 (Pubitemid 44935518)
11. Faca, V.; Pitteri, S. J.; Newcomb, L.; Glukhova, V.; Phanstiel, D.; Krasnoselsky, A.; Zhang, Q.; Struthers, J.; Wang, H.; Eng, J.; Fitzgibbon, M.; McIntosh, M.; Hanash, S. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J. Proteome Res. 2007, 6 (9), 3558-3565 (Pubitemid 47522747)
12. Martosella, J.; Zolotarjova, N.; Liu, H.; Nicol, G.; Boyes, B. E. Reversed-phase high-performance liquid chromatographic prefractionation of immunodepleted human serum proteins to enhance mass spectrometry identification of lower-abundant proteins. J. Proteome Res. 2005, 4 (5), 1522-1537 (Pubitemid 41464777)
13. Stalder, D.; Haeberli, A.; Heller, M. Evaluation of reproducibility of protein identification results after multidimensional human serum protein separation. Proteomics 2008, 8 (3), 414-424. (Pubitemid 351252001)
14. Tang, H. Y.; Ali-Khan, N.; Echan, L. A.; Levenkova, N.; Rux, J. J.; Speicher, D. W. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 2005, 5 (13), 3329-3342 (Pubitemid 41192039)
15. Solassol, J.; Marin, P.; Demettre, E.; Rouanet, P.; Bockaert, J.; Maudelonde, T.; Mange, A. Proteomic detection of prostate-specific antigen using a serum fractionation procedure: potential implication for new low-abundance cancer biomarkers detection. Anal. Biochem. 2005, 338 (1), 26-31. (Pubitemid 40228894)
16. Barnidge, D. R.; Goodmanson, M. K.; Klee, G. G.; Muddiman, D. C. Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-Ms/MS using protein cleavage and isotope dilution mass spectrometry. J. Proteome Res. 2004, 3 (3), 644-652 (Pubitemid 39207371)
17. Wu, S. L.; Amato, H.; Biringer, R.; Choudhary, G.; Shieh, P.; Hancock, W. S. Targeted proteomics of low-level proteins in human plasma by LC/MSn: using human growth hormone as a model system. J. Proteome Res. 2002, 1 (5), 459-465 (Pubitemid 36395865)
18. Yague, J.; Paradela, A.; Ramos, M.; Ogueta, S.; Marina, A.; Barahona, F.; Lopez de Castro, J. A.; Vazquez, J. Peptide rearrangement during quadrupole ion trap fragmentation: added complexity to MS/MS spectra. Anal. Chem. 2003, 75 (6), 1524-1535 (Pubitemid 36397187)
19. Lipton, M. S.; Pasa-Tolic, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore, R. J.; Romine, M. F.; Shen, Y.; Stritmatter, E.; Tolic, N.; Udseth, H. R.; Venkateswaran, A.; Wong, K. K.; Zhao, R.; Smith, R. D. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (17), 11049-11054 (Pubitemid 34920877)
20. Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Pasa-Tolic, L.; Shen, Y.; Conrads, T. P.; Veenstra, T. D.; Udseth, H. R. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2002, 2 (5), 513-523 (Pubitemid 34507341)
21. Omenn, G. S.; States, D. J.; Adamski, M.; Blackwell, T. W.; Menon, R.; Hermjakob, H.; Apweiler, R.; Haab, B. B.; Simpson, R. J.; Eddes, J. S.; Kapp, E. A.; Moritz, R. L.; Chan, D. W.; Rai, A. J.; Admon, A.; Aebersold, R.; Eng, J.; Hancock, W. S.; Hefta, S. A.; Meyer, H.; Paik, Y. K.; Yoo, J. S.; Ping, P.; Pounds, J.; Adkins, J.; Qian, X.; Wang, R.; Wasinger, V.; Wu, C. Y.; Zhao, X.; Zeng, R.; Archakov, A.; Tsugita, A.; Beer, I.; Pandey, A.; Pisano, M.; Andrews, P.; Tammen, H.; Speicher, D. W.; Hanash, S. M. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5 (13), 3226-3245 (Pubitemid 41192032)
22. States, D. J.; Omenn, G. S.; Blackwell, T. W.; Fermin, D.; Eng, J.; Speicher, D. W.; Hanash, S. M. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol. 2006, 24 (3), 333-338 (Pubitemid 43372157)
23. Zhou, M.; Lucas, D. A.; Chan, K. C.; Issaq, H. J.; Petricoin, E. F., 3rd.; Liotta, L. A.; Veenstra, T. D.; Conrads, T. P. An investigation into the human serum "interactome. Electrophoresis 2004, 25 (9), 1289-1298
24. Arnott, D.; Kishiyama, A.; Luis, E. A.; Ludlum, S. G.; Marsters, J. C., Jr.; Stults, J. T. Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot. Mol. Cell. Proteomics 2002, 1 (2), 148-156
25. Blankenship, J. W.; Varfolomeev, E.; Goncharov, T.; Fedorova, A. V.; Kirkpatrick, D. S.; Izrael-Tomasevic, A.; Phu, L.; Arnott, D.; Aghajan, M.; Zobel, K.; Bazan, J. F.; Fairbrother, W. J.; Deshayes, K.; Vucic, D. Ubiquitin binding modulates IAP antagonist-stimulated proteasomal degradation of c-IAP1 and c-IAP2(1). Biochem. J. 2009, 417 (1), 149-160
26. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (12), 6940-6945 (Pubitemid 36706372)
27. Stahl-Zeng, J.; Lange, V.; Ossola, R.; Eckhardt, K.; Krek, W.; Aebersold, R.; Domon, B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 2007, 6 (10), 1809-1817 (Pubitemid 350031682)
28. Brun, V.; Dupuis, A.; Adrait, A.; Marcellin, M.; Thomas, D.; Court, M.; Vandenesch, F.; Garin, J. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell. Proteomics 2007, 6 (12), 2139-2149
29. Hanke, S.; Besir, H.; Oesterhelt, D.; Mann, M. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J. Proteome Res. 2008, 7 (3), 1118-1130