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Review

SELDI proteinchip MS: a platform for biomarker discovery and cancer diagnosis

Pages 549-563 | Published online: 09 Jan 2014

References

  • Gygi SP, Rochon Y, Franza B, Abersold R Correlation between protein and mRNA abundance in yeast. MoZ Cell Biol. 19, 1720–1730 (2002).
  • Keough T, Lacey MP, Fieno, AM et al. Tandem mass spectrometry methods for definitive protein identification in proteomics research. Electrophoresis 21, 2252–2265 (2000).
  • Sriniva PR, Srivastava S, Hanash S, Wright GL Jr. Proteomics in early detection of cancer. Clin. Chem. 47,1901–1911 (2001).
  • Merchant M, Weinberger SR Recent advancements in surface-enhanced laser desorption/ionization—time of flight—mass spectrometry. Electrophoresis 21,1164–1177 (2000).
  • •Describes the SELDI technique, its advancements and future directions.
  • Fung ET, Wright GL Jr, Dalmasso EA. Proteomic strategies for biomarker identification: progress and challenges. Curr. Opin. Mot Then 2,643–650 (2000).
  • Lee KH. Proteomics: a technology- driven and technology-limited discovery science. Trends Biotechnol. 19,217–222 (2001).
  • Fung ET, Thulasiramen V, Weinberger SR, Dalmasso EA. Protein biochips for differential profiling. Curr. Opin. BiotechnoZ 12,65–69 (2001).
  • Figeys, D. Array and lab on a chip technology for protein characterization. Curr. Opin. MoZ Then 1, 685–694 (1999).
  • Guetens G, Van Cauwenberghe K, De Boeck G et aZ Nanotechnology in bio/ clinical analysis. J. Chromatogr. B. Biomed. AppZ 739,139–150 (2002).
  • Weinberger SR, Morris TS, Pawlak M. Recent trends in protein biochip technology. Pharmacogenomics 1, 395–416 (2000).
  • •Describes recent development, advantages and limitations of biochips, including Ciphergen's proteinchip, for the detection and analysis of proteins.
  • Hutchens TW, Yip TT: New desorption strategies for the mass spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom. 7,576–580 (1993).
  • Fung ET, Enderwick C. ProteinChip clinical proteomics: computational challenges and solutions. Bio. Techniques (Suppl.) 34 41 (2002).
  • ••Describes Ciphergen's Pattern MatchingSoftware for classification of clinical samples.
  • Adam B-L, Davis JW, Cazares LH, Schellhammer PF, Wright GL. Identifying the signature proteins of prostate cancer in seminal plasma by SELDI affinity mass spectrometry. Proc. Am. Ass. Cancer Res. 41,564 (2000) (Abstract 3592).
  • Chapman K The ProteinChip Biomarker System from Ciphergen Biosystems: a novel proteomic platform for rapid biomarker discovery and validation. Biochem. Soc. Trans. 30,82–87 (2002).
  • Davies HA. The Protein Chip System from Ciphergen: a new technique for rapid, micro-scale protein biology. J. MoZ Med 78, B29 (2000).
  • Issaq HJ, Veenstra TD, Conrads TP, Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem. Biophys. Res. Commun. 292,587–592 (2002).
  • Weinberger SR, Dalmasso EA, Fung ET. Current achievements using ProteinChip Array technology. Curr. Opin. Chem. Bia 8, 86–91 (2002).
  • Paweletz CP, Charboneau L, Bichsel VE et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20,1981–1989 (2001).
  • Best gm, Emmert-Buck MR Molecular profiling of tissue samples using laser capture microdissection. Expert Rev. Mot Diagn. 1, 53–60 (2001).
  • •Excellent review of advantages and limitations of laser capture microdissection.
  • Simone ML, Paweletz CP, Charboneau L et al. Laser capture microdissection: beyond functional genomics to proteomics. MoZ Diagn. 5,301–307 (2000).
  • von Fading FV, Davies H, Lomas L et al. Tissue-specific microdissection coupled with ProteinChip Array technologies: applications in cancer research. Bio. Techniques 29,1066–1070 (2000).
  • Banks RE, Dunn MJ, Forbes MA et al. The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis — preliminary findings. Electrophoresis 20,689–700 (1999).
  • Paweletz CP, Gillespie JW; Ornstein DK et al. Rapid protein display profiling of cancer progression directly from human tissue using a protein biochip. Drug Dev. Res. 49, 34 42 (2001).
  • Wulfkuhle JD, McLean KC, Paweletz GP et al. New approaches to proteomic analysis of breast cancer. Proteomics 1, 1205–2001 (2001).
  • Paweletz GP, Liotta LA, Petricoin EF III. New technologies for biomarker analysis of prostate cancer progression: laser capture microdissection and tissue-proteomics. Urology 57, 160–163 (2001).
  • Zhukov TA, Johanson R, Tockman MS et al. Discovery of distinct protein profiling specific for lung tumors and pre-malignant lung lesions by SELDI mass spectrometry. Proc. Am. Ass. Cancer Res. 43, 36 (2002) (Abstract 184).
  • Von Eggling F, Junker K, Fiedle Wet al. Mass spectrometry meets chip technology: a new proteomic tool in cancer research? Electrophoresis 22, 2898–2902 (2001).
  • Ball G, Mian S, Holding F et at An integrated approach utilizing artificial neural networks and SELDI mass speactrometry for the classification of human tumors and rapid identification of potential biomarkers. Bioinfirmatics 18, 395–404 (2002).
  • Verma M, Wright GL Jr, Hanash SM, Gopal-Srivastava R, Srivastava S. Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers. Ann. NY Acad. Sci. 945, 103–115 (2001).
  • Wright GL Jr, Cazares LH, Leung S-M et al. ProteinChip surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel proteomic technology for detection of prostate cancer biomarkers in complex protein mixtures. Pros. Cancer Pros. Dis. 2, 264–267 (1999).
  • ••One of the first papers describing thepotential of SELDI for discovery and analysis of cancer-associated protein biomarkers.
  • C.azares LH, Adam B-L, Ward MD et id Normal, benign, pre-neoplastic and malignant prostate cells have distinct protein expression profiles resolved by SELDI mass spectrometry. Clin. Cancer Res. 8, 2541–2552 (2002).
  • Wellmann A, Wollscheid V, Lu H et al. Analysis of microdissected prostate tissue with ProteinChip arrays — a way to new insights into carcinogenesis and to diagnostic tools. Int. J. Mot Med. 9, 341–347 (2002).
  • Paweletz CP, Trock B, Pennanen M et id Proteomic patterns of nipple aspirate fluids obtained by SELDI-TOF: potential for new biomarkers to aid in the diagnosis of breast cancer. Disease Markers 17, 201–307 (2001).
  • Watkins B, Szaro R, Ball S et aZ Detection of early-stage cancer by serum protein analysis. Am. Lab. 32–36 (2001).
  • Roboz J, Ma L, Sung M et al. Protein profiles of serum in colon cancer by SELDI-TOF mass spectrometry. Proc. Am. Ass. Cancer Res. 43, 37 (2002) (Abstract 190).
  • Zhao X, Mao Y, Zhang Let al. Discovery of esophageal cancer protein biomarkers in serum. Proc. Am. Ass. Cancer Res. LB133 (2002).
  • Wu W, Hu W, Hong WK et al. Rapid screening and identification of serum tumor-associated markers in patients with respectable non-small cell lung cancer. Proc. Am. Ass. Cancer Res. 43, 756 (2002) (Abstract 3749).
  • Yip TIC, Yip C, Yiip Vet al. Serum ProteinChip profiling can identify new protein markers in the diagnosis of relapse of nasopharyngeal carcinoma CS Choi-Proc. Am. Ass. Cancer Res. 161 (2002).
  • Ye B, Cramer DW, Pratomo Vet al. A novel ovarian cancer biomarker: Haptoglobin alpha chain, identification and characterization with mass spectrometry and liquid chromatography. Proc. Am. Ass. Cancer Res. 43, 743 (2002) (Abstract 3687).
  • Rusty C, Christa L, Kuzclzal S et al. Identification of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein 1 as a biomarker for pancreatic ductal adeocarcinoma by protein biochip technology. Cancer Res. 62, 1868–1875 (2002).
  • Vlahou A, Schellhammer PF, Mendrinos S et al. Development of a novel proteomic approach for the detection of transitional cell carcinoma of the bladder in urine. Am. Pathot 158, 1491–1502 (2001).
  • Munro NP, Rogers, M Craven RA et aZ Surface enhanced laser deorption/ ionization mass spectrometry and neural network modeling: a proteomic approach to the identification of urinary biomarkers of transitional cell carcinoma.' Ural. 167, 160 (2002) (Abstract 643).
  • Vlahou A, Giannopoulos A, Wilson LL et al. Application of the SELDI ProteinChip® system in bladder cancer diagnosis. Proc. Am. Ass. Cancer Res. 43, 35 (2002) (Abstract 1823).
  • ••Original paper describing SELDI proteinprofiling as a potential clinical assay.
  • Petricoin EF, Ardekani AM, Hitt BA et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572–577 (2002).
  • ••First report describing the successfulcombining of an artificial intelligent algorithm for accurate diagnosis of ovarian cancer.
  • Vlahou A, Gregory BW, Wilson LL et al. SELDI protein profiling in ovarian cancer diagnosis. Proc. Am. Ass. Cancer Res. 43, 36 (2002) (Abstract 183).
  • Zhang Z, Rai AJ, Rosenzweig J et at Comparison of protein profiles in plasma between early and late stage ovarian cancer patients using SELDI protein chip/mass spectrometry. Proc. Am. Ass. Cancer Res. 43, 36 (2002) (Abstract 188).
  • Hu W, Verschraegen CF, Wu Wet aZ Differential protein profile analysis of sera from normal donors and ovarian cancer patients by proteomics. Proc. Am. Ass. Cancer Res. 43, 37 (2002) (Abstract 189).
  • Qu Y, Adam B-L, Thomquist Metal. Data reduction using discrete wavelet transform in discriminant analysis with very high dimension. Biometrics (In Press).
  • Vapnik VX. Statistical Learning Thevry. Springer, NY, USA (1998).
  • Breiman L, Friedman JH, Olshen RA, Stone q. Classification and Regression Trees. Wadsworth International Group, Belmont, CA, USA (1984). SiAdam B-L, Qu Y, Davis JW et at Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res. 62, 3609–3614 (2002).
  • ••Describes the successful use of SELDI protein profiling for the diagnosis of prostate cancer.
  • Qu Y, Adam B-L, Yasui Y et al. Boosted decision tree analysis of SELDI mass spectral serum profiles discriminates prostate cancer from non-cancer patients. Clin. Chem. 48, 1835–1843 (2002).
  • Li J, Zhang Z, Rosenzweig J et aZ Characterization of prostate disease and no-disease groups using serum protein profiles generated by SELDI protein chip/mass spectrometry.' Ural. 167, 287 (2002) (Abstract 1131).
  • Mobley J, Pais VM, Lau K-M et al. Mass profiling of serological proteins combined with data mining algorithms together form a highly sensitive and accurate tool for the diagnosis and characterization of prostate cancer./ Urol. 167, 287 (2002) (Abstract 1130).
  • Ardkani, AM, Hitt, BA, Hackett, PS et al. Nth dimensional proteomic signatures in sera detect ovarian and prostate cancer. Proc. Am. Ass. Cancer Res. 43, 927 (2002) (Abstract 4592).
  • Stamey TA. Preoperative serum prostate specific antigen (PSA) below 10 ig/1, predicts neither the presence of prostate cancer nor the rate of postoperative PSA failure. Clin. Chem. 47, 631–634 (2001).
  • Li J, Zhang Z, Rosenzweig J et aZ Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin. Chem. 48, 1296–1304 (2002).
  • Poon TCW, Yip TT, Yip C et at Application of the surface-enhanced laser desorption ionization (SELDI) ProteinChip Biomarker System to the discovery of serological biomarkers associated with hepatocellular carcinoma. Proc. Am. Ass. Cancer Res. 43, 396–397 (2002) (Abstract 1976).
  • Wang S, Diamond DL, Hass GM et al. Identification of prostate specific membrane antigen (PSMA) as the target of monoclonal antibody 107-1A4 by protein chip array surface-enhanced laser-desorption/ionization (SELDI) technology. Int. J. Cancer 92, 871–876 (2001).
  • Xiao Z, Adam B-L, Cazares LH et aZ Quantitation of serum prostate-specific membrane antigen by a novel protein biochip immunoassay discriminates benign from malignant prostate disease. Cancer Res. 61, 6029–6033 (2001).
  • ••First report describing the developmentand application of a SELDI immunoassay for quantitative measurement of a cancer biotnarker.
  • Wright GL Jr, Grob BM, Petrylak D et al. Upregulation of prostate specific membrane antigen (PSMA) following androgen deprivation therapy. Urology 48, 326–334 (1996).
  • Holmes EH. PSMA specific antibodies and their diagnostic and therapeutic use. Expert Opin. Investig. Drugs 10, 511–519 (2001).
  • Jenkins R, Pennington S. Arrays for protein expression profling: towards a viable alternative to two-dimensional gel electrophoresis. Proteomics 1, 13–29 (2001).
  • Sullivan PM, Etzioni R, Feng Z et aZ Phases of biomarker development for early detection of cancer." Natl. Cancer Inst. 93, 1054–1061 (2001).
  • Leushner J, Chiu NH. Automated mass spectrometry: a revolutionary technology for clinical diagnostics. Mal Diagn. 5, 341–348 (2000).
  • www.chipergen.com
  • http://edm.nci.niti.gov
  • •Describes collaborative program to identify and validate biomarkers for the early detection of cancer using genomic and proteotnic technologies.
  • http://clinicalproteomics.steem.com/ download-prost.php
  • •The raw SELDI data files for ovarian and other cancers are available for viewing and analysis that are obtained at the Clinical Proteomics Program, a joint collaboration between the National Cancer Institute and the Food and Drug Administration.
  • www.correlogic.com
  • http://140.107.129.65/stat_methods.htm
  • •Provides a complete detailed description of the Decision Tree and Boosting Decision Tree algorithms.
  • www.evms.edu/vpc/seldi
  • •Raw SELDI data files for the prostate cancer data set can be accessed for viewing and analysis.
  • www.hupo.org
  • •Recently developed international organization to decipher the human proteome analogous to the human genome project. Presents objectives and goals, planned projects and valuable links to proteotnic databases, proteotnic tools, reports and journals.

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