Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: A systematic review

Journal of Proteome Research

Volumn 7, Issue 4, 2008, Pages 1395-1402

  Callesen, Anne K ^a,b   Vach, Werner ^a   Jørgensen, Per E ^b   Cold, Søren ^b   Mogensen, Ole ^b   Kruse, Torben A ^b   Jensen, Ole N ^a   Madsen, Jonna S ^b  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b ODENSE UNIVERSITY HOSPITAL   (Denmark)

Author keywords

Breast cancer; Mass spectrometry, Systematic review; Protein profiling; Proteomics

Indexed keywords

BIOLOGICAL MARKER; PLASMA PROTEIN;

ARTICLE; BREAST CANCER; CANCER DIAGNOSIS; CLINICAL STUDY; HUMAN; INFORMATION PROCESSING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; REPRODUCIBILITY; SYSTEMATIC REVIEW; VALIDATION STUDY; BLOOD; BREAST TUMOR; CHEMISTRY; COMPARATIVE STUDY; FEMALE; METHODOLOGY; PROTEOMICS; REVIEW; SECRETIONS; STATISTICS;

BLOOD PROTEINS; BODILY SECRETIONS; BREAST NEOPLASMS; FEMALE; HUMANS; MASS SPECTROMETRY; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 45549105194     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800115f     Document Type: Article

References (39)

1. Cho, W. C.; Cheng, C. H. Oncoproteomics: current trends and future perspectives. Expert Rev. Proteomics 2007, 4, 401-410.
2. Diamandis, E. P. Peptidomics for cancer diagnosis: Present and future. J. Proteome Res. 2006, 5, 2079-2082.
3. Li, J.; Zhang, Z.; Rosenzweig, J.; Young, Y.; Chan, D. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem. 2002, 48, 1296-1304.
4. Becker, S.; Cazares, L. H.; Watson, P.; Lynch, H.; Semmes, O. J.; Drake, R. R.; Laronga, C. Surfaced-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer. Ann. Surg. Oncol. 2004, 11, 907-914.
5. Caputo, E.; Lombardi, M. L.; Luongo, V.; Moharram, R.; Tornatore, P.; Pirozzi, G.; Guardiola, J.; Martin, B. M. Peptide profiling in epithelial tumor plasma by the emerging proteomic techniques. J. Chromatogr. B: Anal. Technol. Biomed. Life Sci. 2005, 819, 59-66.
6. Heike, Y.; Hosokawa, M.; Osumi, S.; Fujii, D.; Aogi, K.; Takigawa, N.; Ida, M.; Tajiri, H.; Eguchi, K.; Shiwa, M.; Wakatabe, R.; Arikuni, H.; Takaue, Y.; Takashima, S. Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI ProteinChip system. Anticancer Res. 2005, 25, 1197-1203.
7. Hu, Y.; Zhang, S.; Yu, J.; Liu, J.; Zheng, S. SELDI-TOF-MS: the proteomics and bioinformatics approaches in the diagnosis of breast cancer. Breast 2005, 14, 250-255.
8. Kuerer, H. M.; Coombes, K. R.; Chen, J. N.; Xiao, L.; Clarke, C.; Fritsche, H.; Krishnamurthy, S.; Marcy, S.; Hung, M. C.; Hunt, K. K. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery 2004, 136, 1061-1069.
9. Laronga, C.; Becker, S.; Watson, P.; Gregory, B.; Cazares, L.; Lynch, H.; Perry, R. R.; Wright, G. L., Jr.; Drake, R. R.; Semmes, O. J. SELDI-TOF serum profiling for prognostic and diagnostic classification of breast cancers. Dis. Markers 2003-04, 19, 229-238.
10. Li, J.; Orlandi, R.; White, C. N.; Rosenzweig, J.; Zhao, J.; Seregni, E.; Morelli, D.; Yu, Y.; Meng, X. Y.; Zhang, Z.; Davidson, N. E.; Fung, E. T.; Chan, D. W. Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry. Clin. Chem. 2005, 51, 2229-2235.
11. Li, J.; Zhao, J.; Yu, X.; Lange, J.; Kuerer, H.; Krishnamurthy, S.; Schilling, E.; Khan, S. A.; Sukumar, S.; Chan, D. W. Identification of biomarkers for breast cancer in nipple aspiration and ductal lavage fluid. Clin. Cancer Res. 2005, 11, 8312-8320.
12. Mathelin, C.; Cromer, A.; Wendling, C.; Tomasetto, C.; Rio, M. C. Serum biomarkers for detection of breast cancers: A prospective study. Breast Cancer Res. Treat. 2006, 96, 83-90.
13. Mendrinos, S.; Nolen, J. D.; Styblo, T.; Carlson, G.; Pohl, J.; Lewis, M.; Ritchie, J. Cytologic findings and protein expression profiles associated with ductal carcinoma of the breast in ductal lavage specimens using surface-enhanced laser desorption and ionization-time of flight mass spectrometry. Cancer 2005, 105, 178-183.
14. Paweletz, C. P.; Trock, B.; Pennanen, M.; Tsangaris, T.; Magnant, C.; Liotta, L. A.; Petricoin, E. F. 3rd Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Dis. Markers 2001, 17, 301-307.
15. Pawlik, T. M.; Fritsche, H.; Coombes, K. R.; Xiao, L.; Krishnamurthy, S.; Hunt, K. K.; Pusztai, L.; Chen, J. N.; Clarke, C. H.; Arun, B.; Hung, M. C; Kuerer, H. M. Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry. Breast Cancer Res. Treat. 2005, 89, 49-157.
16. Pusztai, L.; Gregory, B. W.; Baggerly, K. A.; Peng, B.; Koomen, J.; Kuerer, H. M.; Esteva, F. J.; Symmans, W. F.; Wagner, P.; Hortobagyi, G. N.; Laronga, C.; Semmes, O. J. Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma. Cancer 2004, 100, 1814-1822.
17. Sauter, E. R.; Zhu, W.; Fan, X. J.; Wassell, R. P.; Chervoneva, I.; Du Bois, G. C. Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer. Br. J. Cancer 2002, 86, 1440-1443.
18. Sauter, E. R.; Shan, S.; Hewett, J. E.; Speckman, P.; Du Bois, G. C. Proteomic analysis of nipple aspirate fluid using SELDI-TOF-MS. Int. J. Cancer 2005, 114, 791-796.
19. Streckfus, C. F.; Bigler, L. R.; Zwick, M. The use of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry to detect putative breast cancer markers in saliva: a feasibility study. J. Oral. Pathol. Med. 2006, 35, 292-300.
20. Traub, F.; Feist, H.; Kreipe, H. H.; Pich, A. SELDI-MS-based expression profiling of ductal invasive and lobular invasive human breast carcinomas. Pathol. Res. Pract. 2005, 201, 763-770.
21. Vlahou, A.; Laronga, C.; Wilson, L.; Gregory, B.; Fournier, K.; McGaughey, D.; Perry, R. R.; Wright, G. L., Jr.; Semmes, O. J. A novel approach toward development of a rapid blood test for breast cancer. Clin. Breast Cancer 2003, 4, 203-209.
22. Villanueva, J.; Shaffer, D. R.; Philip, J.; Chaparro, C. A.; Erdjument-Bromage, H.; Olshen, A. B.; Fleisher, M.; Lilja, H.; Brogi, E.; Boyd, J.; Sanchez-Carbayo, M.; Holland, E. C. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J. Clin. Invest. 2006, 116, 271-284.
23. Henderson, N. A.; Steele, R. J. SELDI-TOF proteomic analysis and cancer detection. Surgeon 2005, 3, 383-390.
24. Baumann, S.; Ceglarek, U.; Fiedler, G. M.; Lembcke, J.; Leichtle, A.; Thiery, J. Standardized approach to proteome profiling of human serum based on magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem. 2005, 51, 973-980.
25. de Noo, M. E.; Tollenaar, R. A.; Ozalp, A.; Kuppen, P. J.; Bladergroen, M. R.; Eilers, P. H.; Deelder, A. M. Reliability of human serum protein profiles generated with C8 magnetic beads assisted MALDI-TOF mass spectrometry. Anal. Chem. 2005, 77, 7232-7241.
26. Villanueva, J.; Philip, J.; Entenberg, D.; Chaparro, C. A.; Tanwar, M. K.; Holland, E. C; Tempst, P. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 2004, 76, 1560-1570.
27. Callesen, A. K.; Mohammed, S.; Bunkenborg, J.; Kruse, T. A.; Cold, S.; Mogensen, O.; Christensen, R.; Vach, W.; Jørgensen, P. E.; Jensen, O. N. Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 2005, 19, 1578-1586.
28. Baggerly, K. A.; Morris, J. S.; Coombes, K. R. Reproducibility of SELDI TOF protein patterns in serum: comparing data sets from different experiments. Bioinformatics 2004, 20, 777-785.
29. Boguski, M. S.; Mcintosh, M. W. Biomedical informatics for proteomics. Nature 2003, 422, 233-237.
30. Somorjai, R. L.; Dolenko, B.; Baumgartner, R. Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics 2003, 19, 1484-1491.
31. Yasui, Y.; Pepe, M.; Thompson, M. L.; Adam, B. L.; Wright, G. L., Jr.; Qu, Y.; Potter, J. D.; Winget, M.; Thornquist, M.; Feng, Z. A data-analytic strategy for protein biomarker discovery: profiling of high-dimensional proteomic data for cancer detection. Biostatistics 2003, 4, 449-463.
32. Callesen, A. K.; Vach, W.; Jørgensen P. E.; Cold, S.; Tan, Q.; Christensen, R.; Mogensen, O.; Kruse, T. A.; Jensen, O. N.; Madsen, J. S. Combined experimental and statistical strategy for mass spectrometry based serum protein profiling for diagnosis of breast cancer: A case-control study. J. Proteome Res. 2008, 7, 1419-1426.
33. Coombes, K. R. Analysis of mass spectrometry profiles of the serum proteome. Clin. Chem. 2005, 51, 1-2.
34. Bossuyt, P. M.; Reitsma, J. B.; Bruns, D. E.; Gatsonis, C. A.; Glasziou, P. P.; Irwig, L. M.; Lijmer, J. G.; Moher, D.; Rennie, D.; de Wet, H. C. W. Towards complete and accurate reporting of studies of diagnostic accuracy: the STARD initiative. Br. Med. J. 2003, 326, 41-44.
35. Bons, J. A. P.; Wodzig, W. K. W. H.; van Dieijen-Visser, M. P. Protein profiling as a diagnostic tool in clinical chemistry: a review. Clin. Chem. Lab. Med. 2005, 43, 1281-1290.
36. Rai, J. A.; Gelfand, C. A.; Haywood, B. C.; Waiunek, D. J.; Yi, J.; Schuchard, M. D.; Mehigh, R. J.; Cockrill, S. L.; Scott, G. B. I.; Tammen, H.; Sculz-Knappe, P.; Speicher, D. W. HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples. Proteomics 2005, 5, 3262-3277.
37. Sorace, J. M.; Zhan, M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinf. 2003, 4, 24.
38. Bossuyt, P. M.; Reitsma, J. B.; Bruns, D. E.; Gatsonis, C. A.; Glasziou, P. P.; Irwig, L. M.; Lijmer, J. G.; Moher, D.; Rennie, D.; de Wet, H. C. W. Towards complete and accurate reporting of studies of diagnostic accuracy: the STARD initiative. Br. Med. J. 2003, 326, 41-44.
39. Moher, D.; Jones, A.; Lepage, L. Use of the CONSORT statement and quality of reports of randomized trials: a comparative before-and-after evaluation. JAMA, J. Am. Med. Assoc. 2001, 285, 1992-1995.