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Licensed Unlicensed Requires Authentication Published by De Gruyter November 28, 2005

Protein profiling as a diagnostic tool in clinical chemistry: a review

  • Judith A. P. Bons , Will K. W. H. Wodzig and Marja P. van Dieijen-Visser


Serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) appears to be an important diagnostic tool for a whole range of diseases. Sensitivities and specificities obtained with this new technology often seem superior to those obtained with current biomarkers. However, reproducibility and standardization are still problematic. The present review gives an overview of the diagnostic value of protein profiles obtained with SELDI in studies on prostate and ovarian cancer. To identify aspects important for protein profiling, we compare and discuss differences in pre- and post-analytical conditions presented in the literature supplemented with some of our own data. Further progress in protein profiling as a diagnostic tool requires a more comprehensive description of technical details in all future studies.

Corresponding author: M.P. van Dieijen-Visser, Department of Clinical Chemistry, University Hospital Maastricht, PO Box 5800, 6202 AZ Maastricht, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands Phone: +31-43-3876695, Fax: +31-43-3874692,


1. Hutchens TW, Yip T. New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun Mass Spectrom 1993; 7:576–80.10.1002/rcm.1290070703Search in Google Scholar

2. Petricoin I, Emanuel F, Mills GB, Kohn EC, Liotta LA. Proteomic patterns in serum and identification of ovarian cancer. Lancet 2002; 360:170–1.10.1016/S0140-6736(02)09391-1Search in Google Scholar

3. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002; 359:572–7.10.1016/S0140-6736(02)07746-2Search in Google Scholar

4. Kozak KR, Amneus MW, Pusey SM, Su F, Luong MN, Luong SA, et al. Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: potential use in diagnosis and prognosis. Proc Natl Acad Sci USA 2003; 100:12343–8.10.1073/pnas.2033602100Search in Google Scholar PubMed PubMed Central

5. Zhang Z, Bast RC Jr, Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004; 64:5882–90.10.1158/0008-5472.CAN-04-0746Search in Google Scholar PubMed

6. Vlahou A, Schorge JO, Gregory BW, Coleman RL. Diagnosis of ovarian cancer using decision tree classification of mass spectral data. J Biomed Biotechnol 2003; 2003:308–14.10.1155/S1110724303210032Search in Google Scholar PubMed PubMed Central

7. Ye B, Cramer DW, Skates SJ, Gygi SP, Pratomo V, Fu L, et al. Haptoglobin-alpha subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry. Clin Cancer Res 2003; 9:2904–11.Search in Google Scholar

8. Rai AJ, Zhang Z, Rosenzweig J, Shih IM, Pham T, Fung ET, et al. Proteomic approaches to tumor marker discovery. Arch Pathol Lab Med 2002; 126:1518–26.10.5858/2002-126-1518-PATTMDSearch in Google Scholar PubMed

9. Banez LL, Prasanna P, Sun L, Ali A, Zou Z, Adam BL, et al. Diagnostic potential of serum proteomic patterns in prostate cancer. J Urol 2003; 170:442–6.10.1097/01.ju.0000069431.95404.56Search in Google Scholar PubMed

10. Adam BL, Qu Y, Davis JW, Ward MD, Clements MA, Cazares LH, et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 2002; 62:3609–14.Search in Google Scholar

11. Petricoin EF III, Ornstein DK, Paweletz CP, Ardekani A, Hackett PS, Hitt BA, et al. Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 2002; 94:1576–8.10.1093/jnci/94.20.1576Search in Google Scholar PubMed

12. Qu Y, Adam BL, Yasui Y, Ward MD, Cazares LH, Schellhammer PF, et al. Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients. Clin Chem 2002; 48:1835–43.10.1093/clinchem/48.10.1835Search in Google Scholar

13. Li J, White N, Zhang Z, Rosenzweig J, Mangold LA, Partin AW, et al. Detection of prostate cancer using serum proteomics pattern in a histologically confirmed population. J Urol 2004; 171:1782–7.10.1097/01.ju.0000119823.86393.49Search in Google Scholar

14. Zhukov TA, Johanson RA, Cantor AB, Clark RA, Tockman MS. Discovery of distinct protein profiles specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. Lung Cancer 2003; 40:267–79.10.1016/S0169-5002(03)00082-5Search in Google Scholar

15. Poon TC, Hui AY, Chan HL, Ang IL, Chow SM, Wong N, et al. Prediction of liver fibrosis and cirrhosis in chronic hepatitis B infection by serum proteomic fingerprinting: a pilot study. Clin Chem 2004; 51:328–35.10.1373/clinchem.2004.041764Search in Google Scholar PubMed

16. Zhu XD, Zhang WH, Li CL, Xu Y, Liang WJ, Tien P. New serum biomarkers for detection of HBV-induced liver cirrhosis using SELDI protein chip technology. World J Gastroenterol 2004; 10:2327–9.10.3748/wjg.v10.i16.2327Search in Google Scholar PubMed PubMed Central

17. Wiesner A. Detection of tumor markers with ProteinChip technology. Curr Pharm Biotechnol 2004; 5:45–67.10.2174/1389201043489675Search in Google Scholar PubMed

18. Diamandis EP. How are we going to discover new cancer biomarkers? A proteomic approach for bladder cancer. Clin Chem 2004; 50:793–5.10.1373/clinchem.2004.032177Search in Google Scholar PubMed

19. Xiao Z, Prieto D, Conrads TP, Veenstra TD, Issaq HJ. Proteomic patterns: their potential for disease diagnosis. Mol Cell Endocrinol 2005; 230:95–106.10.1016/j.mce.2004.10.010Search in Google Scholar PubMed

20. Belenky A, Smith A, Zhang B, Lin S, Despres N, Wu AH, et al. The effect of class-specific protease inhibitors on the stabilization of B-type natriuretic peptide in human plasma. Clin Chim Acta 2004; 340:163–72.10.1016/j.cccn.2003.10.026Search in Google Scholar PubMed

21. WHO document “Use of anticoagulants in diagnostic laboratory investigations” (WHO/DIL/LAB/99.1 Rev. 2).Search in Google Scholar

22. Solassol J, Marin P, Demettre E, Rouanet P, Bockaert J, Maudelonde T, et al. Proteomic detection of prostate-specific antigen using a serum fractionation procedure: potential implication for new low-abundance cancer biomarkers detection. Anal Biochem 2005; 338:26–31.10.1016/j.ab.2004.11.031Search in Google Scholar PubMed

23. Linke T, Ross AC, Harrison EH. Profiling of rat plasma by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, a novel tool for biomarker discovery in nutrition research. J Chromatogr A 2004; 1043:65–71.10.1016/j.chroma.2004.05.007Search in Google Scholar PubMed

24. Baggerly KA, Morris JS, Coombes KR. Cautions about reproducibility in mass spectrometry patterns: joint analysis of several proteomic data sets., 2003.Search in Google Scholar

25. Malik G, Ward MD, Gupta SK, Trosset MW, Grizzle WE, Adam BL, et al. Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer. Clin Cancer Res 2005; 11:1073–85.10.1158/1078-0432.1073.11.3Search in Google Scholar

26. Wright GL Jr, Cazares LH, Leung SM, Nasim S, Adam BL, Yip TT, et al. Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis 1999; 2:264–76.10.1038/sj.pcan.4500384Search in Google Scholar PubMed

27. Xiao Z, Adam BL, Cazares LH, Clements MA, Davis JW, Schellhammer PF, et al. Quantitation of serum prostate-specific membrane antigen by a novel protein biochip immunoassay discriminates benign from malignant prostate disease. Cancer Res 2001; 61:6029–33.Search in Google Scholar

28. Semmes OJ, Feng Z, Adam BL, Banez LL, Bigbee WL, Campos D, et al. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin Chem 2005; 51:102–12.10.1373/clinchem.2004.038950Search in Google Scholar PubMed

29. Lee SW, Lee KI, Kim JY. Revealing urologic diseases by proteomic techniques. J Chromatogr B 2005; 815:203–13.10.1016/j.jchromb.2004.11.008Search in Google Scholar PubMed

30. Orchard S, Zhu W, Julian RK Jr, Hermjakob H, Apweiler R. Further advances in the development of a data interchange standard for proteomics data. Proteomics 2003; 3:2065–6.10.1002/pmic.200300588Search in Google Scholar PubMed

31. Orchard S, Hermjakob H, Apweiler R. The proteomics standards initiative. Proteomics 2003; 3:1374–6.10.1002/pmic.200300496Search in Google Scholar PubMed

Received: 2005-5-9
Accepted: 2005-7-14
Published Online: 2005-11-28
Published in Print: 2005-12-1

©2005 by Walter de Gruyter Berlin New York

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