Biomarker rediscovery in diagnostics

Bibliography

• National Institutes of Health. Available from: http://www.nih.gov/index.html [Last accessed on August 2008]
   Google Scholar
• National Cancer Institute. Available from: www.cancer.gov [Last accessed on August 2008]
   Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002;1(11):845-67
   PubMed Web of Science ®Google Scholar
• Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 2006;24(8):971-83
   PubMed Web of Science ®Google Scholar
• Anderson NL. The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol Cell Proteomics 2005;4(10):1441-4
   PubMed Web of Science ®Google Scholar
• Peter J, Unverzagt C, Krogh TN, et al. Identification of precursor forms of free prostate-specific antigen in serum of prostate cancer patients by immunosorption and mass spectrometry. Cancer Res 2001;61(3):957-62
   PubMed Web of Science ®Google Scholar
• Mikolajczyk SD, Marker KM, Millar LS, et al. A truncated precursor form of prostate-specific antigen is a more specific serum marker of prostate cancer. Cancer Res 2001;61(18):6958-63
   PubMed Web of Science ®Google Scholar
• Foster DB, Noguchi T, VanBuren P, et al. C-terminal truncation of cardiac troponin I causes divergent effects on ATPase and force: implications for the pathophysiology of myocardial stunning. Circ Res 2003;93(10):917-24
   PubMed Web of Science ®Google Scholar
• Yu ZB, Zhang LF, Jin JP. A proteolytic NH2-terminal truncation of cardiac troponin I that is up-regulated in simulated microgravity. J Biol Chem 2001;276(19):15753-60
   PubMed Web of Science ®Google Scholar
• Wilkins MR, Sanchez JC, Gooley AA, et al. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 1996;13:19-50
   PubMed Web of Science ®Google Scholar
• O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975;250(10):4007-21
   PubMed Web of Science ®Google Scholar
• Gygi SP, Corthals GL, Zhang Y, et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc Natl Acad Sci USA 2000;97(17):9390-5
   PubMed Web of Science ®Google Scholar
• Page JS, Masselon CD, Smith RD. FTICR mass spectrometry for qualitative and quantitative bioanalyses. Curr Opin Biotechnol 2004;15(1):3-11
   PubMed Web of Science ®Google Scholar
• Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19(3):242-7
   PubMed Web of Science ®Google Scholar
• HUPO 3rd World Congress on Proteomics, Beijing, China, October 25th, 2004, Plasma Proteome Session, Available from: http://www.hupo.org/research/files/PPP_January_2003_Omenn.pdf [Viewed August 2008]
   Google Scholar
• Anderson NL, Polanski M, Pieper R, et al. The human plasma proteome: a nonredundant list developed by combination of four separate sources. Mol Cell Proteomics 2004;3(4):311-26
   PubMed Web of Science ®Google Scholar
• Liotta LA, Kohn EC, Petricoin EF. Clinical proteomics: personalized molecular medicine. Jama 2001;286(18):2211-4
   PubMed Web of Science ®Google Scholar
• Petricoin EF, Zoon KC, Kohn EC, et al. Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 2002;1(9):683-95
   PubMed Web of Science ®Google Scholar
• Krieg RC, Paweletz CP, Liotta LA, Petricoin EF, 3rd. Clinical proteomics for cancer biomarker discovery and therapeutic targeting. Technol Cancer Res Treat 2002;1(4):263-72
   PubMed Web of Science ®Google Scholar
• Issaq HJ, Conrads TP, Prieto DA, et al. SELDI-TOF MS for diagnostic proteomics. Anal Chem 2003;75(7):A148-55
   PubMed Web of Science ®Google Scholar
• Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. Mass Spectrom Rev 2004;23(1):34-44
   PubMed Web of Science ®Google Scholar
• Kuwata H, Yip TT, Yip CL, et al. Bactericidal domain of lactoferrin: detection, quantitation, and characterization of lactoferricin in serum by SELDI affinity mass spectrometry. Biochem Biophys Res Commun 1998;245(3):764-73
   PubMed Web of Science ®Google Scholar
• Petricoin EF, Ardekani AM, Hitt BA, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359(9306):572-7
   PubMed Web of Science ®Google Scholar
• Chen YD, Zheng S, Yu JK, Hu X. Artificial neural networks analysis of surface-enhanced laser desorption/ionization mass spectra of serum protein pattern distinguishes colorectal cancer from healthy population. Clin Cancer Res 2004;10(24):8380-5
   PubMed Web of Science ®Google Scholar
• 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(4 Pt 1):1302-5
   PubMed Web of Science ®Google Scholar
• Koopmann J, Zhang Z, White N, et al. Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry. Clin Cancer Res 2004;10(3):860-8
   PubMed Web of Science ®Google Scholar
• Junker K, Gneist J, Melle C, et al. Identification of protein pattern in kidney cancer using ProteinChip(R) arrays and bioinformatics. Int J Mol Med 2005;15(2):285-90
   PubMed Web of Science ®Google Scholar
• Kang X, Xu Y, Wu X, et al. Proteomic fingerprints for potential application to early diagnosis of severe acute respiratory syndrome. Clin Chem 2005;51(1):56-64
   PubMed Web of Science ®Google Scholar
• Shiwa M, Nishimura Y, Wakatabe R, et al. Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform. Biochem Biophys Res Commun 2003;309(1):18-25
   PubMed Web of Science ®Google Scholar
• Wulfkuhle JD, Liotta LA, Petricoin EF. Proteomic applications for the early detection of cancer. Nat Rev Cancer 2003;3(4):267-75
   PubMed Web of Science ®Google Scholar
• Petricoin E, Wulfkuhle J, Espina V, Liotta LA. Clinical proteomics: revolutionizing disease detection and patient tailoring therapy. J Proteome Res 2004;3(2):209-17
   PubMed Web of Science ®Google Scholar
• Petricoin EF, Fishman DA, Conrads TP, et al. Lessons from Kitty Hawk: from feasibility to routine clinical use for the field of proteomic pattern diagnostics. Proteomics 2004;4(8):2357-60
   PubMed Web of Science ®Google Scholar
• Johann DJ, Jr, Mc Guigan MD, Patel AR, et al. Clinical proteomics and biomarker discovery. Ann NY Acad Sci 2004;1022:295-305
   PubMed Web of Science ®Google Scholar
• Rockhill B. Proteomic patterns in serum and identification of ovarian cancer. Lancet 2002;360(9327):169; author reply 70-1
   PubMed Web of Science ®Google Scholar
• Pearl DC. Proteomic patterns in serum and identification of ovarian cancer. Lancet 2002;360(9327):169-70; author reply 70-1
   PubMed Web of Science ®Google Scholar
• Elwood M. Proteomic patterns in serum and identification of ovarian cancer. Lancet 2002;360(9327):170; author reply -1
   PubMed Web of Science ®Google Scholar
• Sorace JM, Zhan M. A data review and re-assessment of ovarian cancer serum proteomic profiling. BMC Bioinformatics 2003;4(1):24
   PubMed Web of Science ®Google Scholar
• Baggerly KA, Morris JS, Edmonson SR, Coombes KR. Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst 2005;97(4):307-9
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Point: Proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin Chem 2003;49(8):1272-5
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Analysis of serum proteomic patterns for early cancer diagnosis: drawing attention to potential problems. J Natl Cancer Inst 2004;96(5):353-6
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol Cell Proteomics 2004;3(4):367-78
   PubMed Web of Science ®Google Scholar
• Diamandis EP. Proteomic patterns to identify ovarian cancer: 3 years on. Expert Rev Mol Diagn 2004;4(5):575-7
   PubMed Web of Science ®Google Scholar
• Coombes KR, Morris JS, Hu J, et al. Serum proteomics profiling-a young technology begins to mature. Nat Biotechnol 2005;23(3):291-2
   PubMed Web of Science ®Google Scholar
• Ransohoff DF. Lessons from controversy: ovarian cancer screening and serum proteomics. J Natl Cancer Inst 2005;97(4):315-9
   PubMed Web of Science ®Google Scholar
• Zhang Z, Bast RC, Jr., Yu Y, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004;64(16):5882-90
   PubMed Web of Science ®Google Scholar
• Paradis V, Degos F, Dargere D, et al. Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases. Hepatology 2005;41(1):40-7
   PubMed Web of Science ®Google Scholar
• Tolson J, Bogumil R, Brunst E, et al. Serum protein profiling by SELDI mass spectrometry: detection of multiple variants of serum amyloid alpha in renal cancer patients. Lab Invest 2004;84(7):845-56
   PubMed Web of Science ®Google Scholar
• Cho WC, Yip TT, Yip C, et al. Identification of serum amyloid a protein as a potentially useful biomarker to monitor relapse of nasopharyngeal cancer by serum proteomic profiling. Clin Cancer Res 2004;10(1 Pt 1):43-52
   PubMed Web of Science ®Google Scholar
• Le L, Chi K, Tyldesley S, et al. Identification of Serum Amyloid A as a Biomarker to Distinguish Prostate Cancer Patients with Bone Lesions. Clin Chem 2005;51(4):695-707
   PubMed Web of Science ®Google Scholar
• Howard BA, Wang MZ, Campa MJ, et al. Identification and validation of a potential lung cancer serum biomarker detected by matrix-assisted laser desorption/ionization-time of flight spectra analysis. Proteomics 2003;3(9):1720-4
   PubMed Web of Science ®Google Scholar
• Koomen JM, Shih LN, Coombes KR, et al. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res 2005;11(3):1110-8
   PubMed Web of Science ®Google Scholar
• Baumann H, Gauldie J. The acute phase response. Immunol Today 1994;15(2):74-80
   PubMedGoogle Scholar
• Kushner I. The phenomenon of the acute phase response. Ann NY Acad Sci 1982;389:39-48
   PubMed Web of Science ®Google Scholar
• Nedelkov D, Tubbs KA, Niederkofler EE, et al. High-Throughput Comprehensive Analysis of Human Plasma Proteins: A Step toward Population Proteomics. Anal Chem 2004;76(6):1733-7
   PubMed Web of Science ®Google Scholar
• Nedelkov D, Kiernan UA, Niederkofler EE, et al. Investigating diversity in human plasma proteins. Proc Natl Acad Sci USA 2005;102(31):10852-7
   PubMed Web of Science ®Google Scholar
• Craig WY, Ledue TB, Ritchie RF. Plasma proteins: Clinical utility and interpretation. Scarborough, ME: Foundation for Blood Research, 2001
   Google Scholar
• Ritchie RF, editor,. Serum Proteins in Clinical Medicine. Scarborough, ME: Foundation for Blood Research 1999
   Google Scholar
• Chakraborty A, Regnier FE. Global internal standard technology for comparative proteomics. J Chromatogr A 2002;949(1-2):173-84
   PubMed Web of Science ®Google Scholar
• Schmidt A, Kellermann J, Lottspeich F. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005;5(1):4-15
   PubMed Web of Science ®Google Scholar
• Gygi SP, Rist B, Gerber SA, et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999;17(10):994-9
   PubMed Web of Science ®Google Scholar
• Steel LF, Haab BB, Hanash SM. Methods of comparative proteomic profiling for disease diagnostics. J Chromatogr B Analyt Technol Biomed Life Sci 2005;815(1-2):275-84
   PubMed Web of Science ®Google Scholar
• Villanueva J, Philip J, Entenberg D, et al. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal Chem 2004;76(6):1560-70
   PubMed Web of Science ®Google Scholar
• Zhang X, Leung SM, Morris CR, Shigenaga MK. Evaluation of a novel, integrated approach using functionalized magnetic beads, bench-top MALDI-TOF-MS with prestructured sample supports, and pattern recognition software for profiling potential biomarkers in human plasma. J Biomol Tech 2004;15(3):167-75
   PubMedGoogle Scholar
• Stoeckli M, Chaurand P, Hallahan DE, Caprioli RM. Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat Med 2001;7(4):493-6
   PubMed Web of Science ®Google Scholar
• Engvall E, Perlmann P. Enzyme-linked immunosorbent assay (ELISA). Quantitative assay of immunoglobulin G. Immunochemistry 1971;8(9):871-4
   PubMedGoogle Scholar
• Van Weemen BK, Schuurs AH. Immunoassay using antigen-enzyme conjugates. FEBS Lett 1971;15(3):232-6
   PubMed Web of Science ®Google Scholar
• Nelson RW, Krone JR, Bieber AL, Williams P. Mass-Spectrometric Immunoassay. Anal Chem 1995;67(7):1153-8
   PubMed Web of Science ®Google Scholar
• Niederkofler EE, Tubbs KA, Gruber K, et al. Determination of beta-2 microglobulin levels in plasma using a high-throughput mass spectrometric immunoassay system. Anal Chem 2001;73(14):3294-9
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Tubbs KA, Gruber K, et al. High-Throughput Protein Characterization Using Mass Spectrometric Immunoassay. Anal Biochem 2002;301(1):49-56
   PubMed Web of Science ®Google Scholar
• Nedelkov D. Population proteomics: addressing protein diversity in humans. Expert Rev Proteomics 2005;2(3):315-24
   PubMed Web of Science ®Google Scholar
• Tubbs KA, Nedelkov D, Nelson RW. Detection and quantification of beta-2-microglobulin using mass spectrometric immunoassay. Anal Biochem 2001;289(1):26-35
   PubMed Web of Science ®Google Scholar
• Tubbs KA, Kiernan UA, Niederkofler EE, et al. Development of recombinant-based mass spectrometric immunoassay with application to resistin expression profiling. Anal Chem 2006;78(10):3271-6
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Addobbati R, Nedelkov D, Nelson RW. Quantitative multiplexed C-reactive protein mass spectrometric immunoassay. J Proteome Res 2006;5(7):1682-7
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Nedelkov D, Nelson RW. Multiplexed mass spectrometric immunoassay in biomarker research: a novel approach to the determination of a myocardial infarct. J Proteome Res 2006;5(11):2928-34
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Tubbs KA, Nedelkov D, et al. Comparative urine protein phenotyping using mass spectrometric immunoassay. J Proteome Res 2003;2(2):191-7
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Tubbs KA, Nedelkov D, et al. Comparative phenotypic analyses of human plasma and urinary retinol binding protein using mass spectrometric immunoassay. Biochem Biophys Res Commun 2002;297(2):401-5
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Tubbs KA, Nedelkov D, et al. Detection of novel truncated forms of human serum amyloid A protein in human plasma. FEBS Lett 2003;537(1-3):166-70
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Nedelkov D, Tubbs KA, et al. Selected Expression Profiling of Full-Length Proteins and Their Variants in Human Plasma. Clin Proteomics J 2004;1(1):7-16
   Google Scholar
• Theberge R, Connors L, Skinner M, et al. Characterization of transthyretin mutants from serum using immunoprecipitation, HPLC/electrospray ionization and matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 1999;71(2):452-9
   PubMed Web of Science ®Google Scholar
• Lacey JM, Bergen HR, Magera MJ, et al. Rapid determination of transferrin isoforms by immunoaffinity liquid chromatography and electrospray mass spectrometry. Clin Chem 2001;47(3):513-8
   PubMed Web of Science ®Google Scholar
• Sen JW, Bergen HR, 3rd, Heegaard NH. On-line immunoaffinity-liquid chromatography-mass spectrometry for identification of amyloid disease markers in biological fluids. Anal Chem 2003;75(5):1196-202
   PubMed Web of Science ®Google Scholar
• Xiao Z, Adam BL, Cazares LH, 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(16):6029-33
   PubMed Web of Science ®Google Scholar
• Nedelkov D, Phillips DA, Tubbs KA, Nelson RW. Investigation of human protein variants and their frequency in the general population. Mol Cell Proteomics 2007;6(7):1183-7
   PubMed Web of Science ®Google Scholar
• Kiernan UA, Nedelkov D, Tubbs KA, et al. Proteomic characterization of novel serum amyloid P component variants from human plasma and urine. Proteomics 2004;4(6):1825-9
   PubMed Web of Science ®Google Scholar
• Jaconi S, Rose K, Hughes GJ, et al. Characterization of two post-translationally processed forms of human serum retinol-binding protein: altered ratios in chronic renal failure. J Lipid Res 1995;36(6):1247-53
   PubMed Web of Science ®Google Scholar
• Graham TE, Yang Q, Bluher M, et al. Retinol-binding protein 4 and insulin resistance in lean, obese, and diabetic subjects. N Engl J Med 2006;354(24):2552-63
   PubMed Web of Science ®Google Scholar
• Baker M. New-wave diagnostics. Nat Biotechnol 2006;24(8):931-8
   PubMed Web of Science ®Google Scholar