Seminars in Radiation Oncology
Volume 18, Issue 2 , Pages 115-125 , April 2008

Proteomics: Methodologies and Applications in Oncology

  • Bradly G. Wouters, PhD

      Affiliations

    • Corresponding Author InformationAddress reprint requests to Bradly G. Wouters, PhD, Department of Radiation Oncology (Maastro Lab), Maastricht University, Universiteitssingel 50, PO Box 616, 6200 MD Maastricht, The Netherlands.

References 

  1. Anderson NL, Anderson NG. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics. 2002;1:845–867
  2. Sjoblom T, Jones S, Wood LD, et al. The consensus coding sequences of human breast and colorectal cancers. Science. 2006;314:268–274
  3. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57–70
  4. Petricoin EF, Espina V, Araujo RP, et al. Phosphoprotein pathway mapping: akt/mammalian target of rapamycin activation is negatively associated with childhood rhabdomyosarcoma survival. Cancer Res. 2007;67:3431–3440
  5. Fenn JB, Mann M, Meng CK, et al. Electrospray ionization for mass spectrometry of large biomolecules. Science. 1989;246:64–71
  6. Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem. 1988;60:2299–2301
  7. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422:198–207
  8. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006;312:212–217
  9. Baldwin MA. Protein identification by mass spectrometry: issues to be considered. Mol Cell Proteomics. 2004;3:1–9
  10. Carr S, Aebersold R, Baldwin M, et al. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics. 2004;3:531–533
  11. Keller A, Nesvizhskii AI, Kolker E, et al. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002;74:5383–5392
  12. Lam H, Deutsch EW, Eddes JS, et al. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics. 2007;7:655–667
  13. Domon B, Aebersold R. Challenges and opportunities in proteomics data analysis. Mol Cell Proteomics. 2006;5:1921–1926
  14. Shiio Y, Aebersold R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc. 2006;1:139–145
  15. Li XJ, Pedrioli PG, Eng J, et al. A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry. Anal Chem. 2004;76:3856–3860
  16. Kuster B, Schirle M, Mallick P, et al. Scoring proteomes with proteotypic peptide probes. Nat Rev Mol Cell Biol. 2005;6:577–583
  17. Mallick P, Schirle M, Chen SS, et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007;25:125–131
  18. Desiere F, Deutsch EW, King NL, et al. The PeptideAtlas project. Nucleic Acids Res. 2006;34(Database issue):D655–D6558
  19. Haab BB. Methods and applications of antibody microarrays in cancer research. Proteomics. 2003;3:2116–2122
  20. Liotta LA, Espina V, Mehta AI, et al. Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell. 2003;3:317–325
  21. Oh P, Li Y, Yu J, et al. Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature. 2004;429:629–635
  22. Allal AS, Kahne T, Reverdin AK, et al. Radioresistance-related proteins in rectal cancer. Proteomics. 2004;4:2261–2269
  23. Hamelinck D, Zhou H, Li L, et al. Optimized normalization for antibody microarrays and application to serum-protein profiling. Mol Cell Proteomics. 2005;4:773–784
  24. Miller JC, Zhou H, Kwekel J, et al. Antibody microarray profiling of human prostate cancer sera: Aantibody screening and identification of potential biomarkers. Proteomics. 2003;3:56–63
  25. Zhou H, Bouwman K, Schotanus M, et al. Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biol. 2004;5:R28
  26. Chi JT, Wang Z, Nuyten DS, et al. Gene expression programs in response to hypoxia: Cell type specificity and prognostic significance in human cancers. PLoS Med. 2006;3:e47
  27. Koritzinsky M, Seigneuric R, Magagnin MG, et al. The hypoxic proteome is influenced by gene-specific changes in mRNA translation. Radiother Oncol. 2005;76:177–186
  28. Han YH, Xia L, Song LP, et al. Comparative proteomic analysis of hypoxia-treated and untreated human leukemic U937 cells. Proteomics. 2006;6:3262–3274
  29. Yang F, Stenoien DL, Strittmatter EF, et al. Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation. J Proteome Res. 2006;5:1252–1260
  30. Flory MR, Lee H, Bonneau R, et al. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 2006;6:6146–6157
  31. Liotta LA, Petricoin EF. Serum peptidome for cancer detection: Spinning biologic trash into diagnostic gold. J Clin Invest. 2006;116:26–30
  32. Petricoin EF, Ardekani AM, Hitt BA, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet. 2002;359:572–577
  33. Petricoin EF, Ornstein DK, Paweletz CP, et al. Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst. 2002;94:1576–1578
  34. Ornstein DK, Rayford W, Fusaro VA, et al. Serum proteomic profiling can discriminate prostate cancer from benign prostates in men with total prostate specific antigen levels between 2.5 and 15.0 ng/ml. J Urol. 2004;172:1302–1305
  35. Adam BL, Qu Y, Davis JW, et al. Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 2002;62:3609–3614
  36. Li J, Zhang Z, Rosenzweig J, et al. Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem. 2002;48:1296–1304
  37. Ebert MP, Meuer J, Wiemer JC, et al. Identification of gastric cancer patients by serum protein profiling. J Proteome Res. 2004;3:1261–1266
  38. Diamandis EP. Point: Proteomic patterns in biological fluids: Do they represent the future of cancer diagnostics?. Clin Chem. 2003;49:1272–1275
  39. Sorace JM, Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics. 2003;4:24
  40. Villanueva J, Shaffer DR, Philip J, et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest. 2006;116:271–284
  41. Lowenthal MS, Mehta AI, Frogale K, et al. Analysis of albumin-associated peptides and proteins from ovarian cancer patients. Clin Chem. 2005;51:1933–1945
  42. Petricoin EF, Belluco C, Araujo RP, et al. The blood peptidome: A higher dimension of information content for cancer biomarker discovery. Nat Rev Cancer. 2006;6:961–967
  43. Simone NL, Paweletz CP, Charboneau L, et al. Laser capture microdissection: Beyond functional genomics to proteomics. Mol Diagn. 2000;5:301–307
  44. Stoeckli M, Chaurand P, Hallahan DE, et al. Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues. Nat Med. 2001;7:493–496
  45. Meier MA, de Gans BJ, van den Berg AM, et al. Automated multiple-layer spotting for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of synthetic polymers utilizing ink-jet printing technology. Rapid Commun Mass Spectrom. 2003;17:2349–2353
  46. Yanagisawa K, Shyr Y, Xu BJ, et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet. 2003;362:433–439
  47. Rai AJ, Gelfand CA, Haywood BC, et al. HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples. Proteomics. 2005;5:3262–3277
  48. Rai AJ, Vitzthum F. Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics. Expert Rev Proteomics. 2006;3:409–426
  49. Timms JF, Arslan-Low E, Gentry-Maharaj A, et al. Preanalytic influence of sample handling on SELDI-TOF serum protein profiles. Clin Chem. 2007;53:645–656
  50. West-Nielsen M, Hogdall EV, Marchiori E, et al. Sample handling for mass spectrometric proteomic investigations of human sera. Anal Chem. 2005;77:5114–5123
  51. West-Norager M, Kelstrup CD, Schou C, et al. Unravelling in vitro variables of major importance for the outcome of mass spectrometry-based serum proteomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2007;847:30–37

 Supported in part by support from the Dutch Science Organization (ZonMW-NWO Top grant 912-03-047 to BW), the Dutch Cancer Society (KWF grant UM 2003-2821 to BW), and the EU 6th framework program (Euroxy program to BW).

PII: S1053-4296(07)00099-9

doi: 10.1016/j.semradonc.2007.10.008

Seminars in Radiation Oncology
Volume 18, Issue 2 , Pages 115-125 , April 2008

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