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Review

Oncoproteomics: current trends and future perspectives

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Pages 401-410 | Published online: 09 Jan 2014

References

  • Anderson L, Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis18, 533–537 (1997).
  • Abbott A. A post-genomic challenge: learning to read patterns of protein synthesis. Nature402, 715–720 (1999).
  • Xiao Z, Prieto D, Conrads TP et al. Proteomic patterns: their potential for disease diagnosis. Mol. Cell. Endocrinol.230(1–2), 95–106 (2005).
  • Cho WC. Proteomics – leading biological science in the 21st Century. Sci. J.56(5), 14–17 (2004).
  • O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem.250, 4007–4021 (1975).
  • Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik26(3), 231–243 (1975).
  • Gygi SP, Corthals GL, Zhang Y et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl Acad. Sci. USA97(17), 9390–9395 (2000).
  • Bjellqvist B, Ek K, Righetti PG et al. Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J. Biochem. Biophys. Methods6(4), 317–339 (1982).
  • Gorg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics4(12), 3665–3685 (2004).
  • Nilsson CL, Larsson T, Gustafsson E et al. Identification of protein vaccine candidates from Helicobacter pylori using a preparative two-dimensional electrophoretic procedure and mass spectrometry. Anal. Chem.72, 2148–2153 (2000).
  • Diamandis EP. Peptidomics for cancer diagnosis: present and future. J. Proteome Res.5(9), 2079–2082 (2006).
  • Shen YF, Smith RD. Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics. Expert Rev. Proteomics2(3), 431–447 (2005).
  • Qian WJ, Jacobs JM, Liu T et al. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol. Cell. Proteomics5(10), 1727–1744 (2006).
  • Min HK, Hyung SW, Shin JW et al. Ultrahigh-pressure dual online solid phase extraction/capillary reversed-phase liquid chromatography/tandem mass spectrometry (DO-SPE/cRPLC/MS/MS): a versatile separation platform for high-throughput and highly sensitive proteomic analyses. Electrophoresis28(6), 1012–1021 (2007).
  • Guo T, Lee CS, Wang W et al. Capillary separations enabling tissue proteomics-based biomarker discovery. Electrophoresis27(18), 3523–3532 (2006).
  • Hoffman SA, Joo WA, Echan LA et al. Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.849(1–2), 43–52 (2007).
  • Marcus K, Schafer H, Klaus S et al. A new fast method for nanoLC-MALDI-TOF/TOF-MS analysis using monolithic columns for peptide preconcentration and separation in proteomic studies. J. Proteome Res.6(2), 636–643 (2007).
  • Imami K, Monton MR, Ishihama Y et al. Simple on-line sample preconcentration technique for peptides based on dynamic pH junction in capillary electrophoresis-mass spectrometry. J. Chromatogr. A.1148(2), 250–255 (2007).
  • Hu Q, Cooks RG, Noll RJ. Phase-enhanced selective ion ejection in an Orbitrap mass spectrometer. J. Am. Soc. Mass Spectrom.18(6), 980–983 (2007).
  • Venable JD, Wohlschlegel J, McClatchy DB et al. Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Anal. Chem.79(8), 3056–3064 (2007).
  • Macek B, Waanders LF, Olsen JV et al. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell. Proteomics5(5), 949–958 (2006).
  • Lim MS, Elenitoba-Johnson KS. Proteomics in pathology research. Lab. Invest.84, 1227–1244 (2004).
  • Everley PA, Bakalarski CE, Elias JE et al. Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. J. Proteome Res.5(5), 1224–1231 (2006).
  • Adachi J, Kumar C, Zhang Y et al. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol.7(9), R80 (2006).
  • Melanson JE, Chisholm KA, Pinto DM. Targeted comparative proteomics by liquid chromatography/matrix-assisted laser desorption/ionization triple-quadrupole mass spectrometry. Rapid Commun. Mass Spectrom.20(5), 904–910 (2006).
  • Liu H, Sadygov RG, Yates JR III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem.76(14), 4193–4201 (2004).
  • Ishihama Y, Oda Y, Tabata T et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics4(9), 1265–1272 (2005).
  • Mayya V, Rezual K, Wu L et al. Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol. Cell. Proteomics5(6), 1146–1157 (2006).
  • Yu Z, Weinberger PM, Sasaki C et al. Phosphorylation of Akt (Ser473) predicts poor clinical outcome in oropharyngeal squamous cell cancer. Cancer Epidemiol. Biomarkers Prev.16(3), 553–558 (2007).
  • Cho WC. Research progress in SELDI-TOF MS and its clinical applications. Chin. J. Biotechnol.22(6), 871–876 (2006).
  • Issaq HJ, Veenstra TD, Conrads TP et al. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem. Biophys. Res. Commun.292, 587–592 (2002).
  • Yanagisawa K, Shyr Y, Xu BJ et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet362(9382), 433–439 (2003).
  • Wong DT. Salivary diagnostics powered by nanotechnologies, proteomics and genomics. J. Am. Dent. Assoc.137(3), 313–321 (2006).
  • Fung ET, Thulasiraman V, Weinberger SR et al. Protein biochips for differential profiling. Curr. Opin. Biotechnol.12, 65–69 (2001).
  • Henderson NA, Steele RJ. SELDI-TOF proteomic analysis and cancer detection. Surgeon3(6), 383–390, 422 (2005).
  • Ajikumar PK, Ng JK, Tang YC et al. Carboxyl-terminated dendrimer-coated bioactive interface for protein microarray: high-sensitivity detection of antigen in complex biological samples. Langmuir23(10), 5670–5677 (2007).
  • Xu R, Gan X, Fang Y et al. A simple, rapid, and sensitive integrated protein microarray for simultaneous detection of multiple antigens and antibodies of five human hepatitis viruses (HBV, HCV, HDV, HEV, and HGV). Anal. Biochem.362(1), 69–75 (2007).
  • Song S, Li B, Wang L et al. A cancer protein microarray platform using antibody fragments and its clinical applications. Mol. Biosyst.3(2), 151–158 (2007).
  • Pepe MS, Cai T, Longton G. Combining predictors for classification using the area under the receiver operating characteristic curve. Biometrics62(1), 221–229 (2006).
  • Fung ET, Enderwick C. ProteinChip clinical proteomics: computational challenges and solutions. BioTechniques Suppl.34–38, 40–41 (2002).
  • Zhang X, Lu X, Shi Q et al. Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics7, 197 (2006).
  • Wang Y, Hanley R, Klemke RL. Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer. J. Proteome Res.5(4), 907–915 (2006).
  • Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol.24(8), 971–983 (2006).
  • Kraljevic S, Sedic M, Scott M et al. Casting light on molecular events underlying anti-cancer drug treatment: what can be seen from the proteomics point of view? Cancer Treat. Rev.32(8), 619–629 (2006).
  • Nettikadan S, Radke K, Johnson J et al. Detection and quantification of protein biomarkers from fewer than 10 cells. Mol. Cell. Proteomics5(5), 895–901 (2006).
  • Granger J, Siddiqui J, Copeland S et al. Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics5(18), 4713–4718 (2005).
  • Omenn GS. Strategies for plasma proteomic profiling of cancers. Proteomics6(20), 5662–5673 (2006).
  • Feuerstein I, Rainer M, Bernardo K et al. Derivatized cellulose combined with MALDI-TOF MS: a new tool for serum protein profiling. J. Proteome Res.4(6), 2320–2326 (2005).
  • Thulasiraman V, Lin S, Gheorghiu L et al. Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands. Electrophoresis26(18), 3561–3571 (2005).
  • van der Merwe DE, Oikonomopoulou K, Marshall J et al. Mass spectrometry: uncovering the cancer proteome for diagnostics. Adv. Cancer Res.96, 23–50 (2007).
  • Finnskog D, Jaras K, Ressine A et al. High-speed biomarker identification utilizing porous silicon nanovial arrays and MALDI-TOF mass spectrometry. Electrophoresis27(5–6), 1093–1103 (2006).
  • Bouamrani A, Ternier J, Ratel D et al. Direct-tissue SELDI-TOF mass spectrometry analysis: a new application for clinical proteomics. Clin. Chem.52(11), 2103–2106 (2006).
  • Hwang SI, Thumar J, Lundgren DH et al. Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene26(1), 65–76 (2007).
  • Danna EA, Nolan GP. Transcending the biomarker mindset: deciphering disease mechanisms at the single cell level. Curr. Opin. Chem. Biol.10(1), 20–27 (2006).
  • Irish JM, Kotecha N, Nolan GP. Mapping normal and cancer cell signalling networks: towards single-cell proteomics. Nat. Rev. Cancer6(2), 146–155 (2006).
  • Griffin JL, Kauppinen RA. Tumour metabolomics in animal models of human cancer. J. Proteome Res.6(2), 498–505 (2007).
  • Fan TW, Lane AN, Higashi RM. The promise of metabolomics in cancer molecular therapeutics. Curr. Opin. Mol. Ther.6(6), 584–592 (2004).
  • Downes MR, Byrne JC, Dunn MJ et al. Application of proteomic strategies to the identification of urinary biomarkers for prostate cancer: a review. Biomarkers11(5), 406–416 (2006).
  • Gogoi R, Srinivasan S, Fishman DA. Progress in biomarker discovery for diagnostic testing in epithelial ovarian cancer. Expert Rev. Mol. Diagn.6(4), 627–637 (2006).
  • Cekaite L, Hovig E, Sioud M. Protein arrays: a versatile toolbox for target identification and monitoring of patient immune responses. Methods Mol. Biol.360, 335–348 (2007).
  • Cho WC. Nasopharyngeal carcinoma: molecular biomarker discovery and progress. Mol. Cancer6, 1 (2007).
  • Cho WC. Contribution of oncoproteomics to cancer biomarker discovery. Mol. Cancer6, 25 (2007).
  • Chuthapisith S, Layfield R, Kerr ID et al. Principles of proteomics and its applications in cancer. Surgeon5(1), 14–22 (2007).
  • Kikuchi T, Carbone DP. Proteomics analysis in lung cancer: challenges and opportunities. Respirology12(1), 22–28 (2007).

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