106
Views
14
CrossRef citations to date
0
Altmetric
Review

Studying multiple protein profiles over time to assess biomarker validity

, , , &
Pages 455-464 | Published online: 09 Jan 2014

References

  • Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics1(11), 845–867 (2002).
  • Adkins JN, Varnum SM, Auberry KJ et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol. Cell. Proteomics1(12), 947–955 (2002).
  • Pieper R, Gatlin CL, Makusky AJ et al. The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics,3(7), 1345–1364 (2003).
  • 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,3(4), 311–326 (2004).
  • Liotta LA, Ferrari M, Petricoin E. Clinical proteomics: written in blood. Nature,425(6961), 905 (2003).
  • Petricoin EF, Liotta LA. Mass spectrometry-based diagnostics: the upcoming revolution in disease detection. Clin. Chem.49(4), 533–534 (2003).
  • Merchant M, Weinberger SR. Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis21(6), 1164–1177 (2000).
  • 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.62(13), 3609–3614 (2002).
  • Honda K, Hayashida Y, Umaki T et al. Possible detection of pancreatic cancer by plasma protein profiling. Cancer Res.65(22), 10613–10622 (2005).
  • Jacquemier J, Ginestier C, Rougemont J et al. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res.65(3), 767–779 (2005).
  • Li Y, Dang TA, Shen J et al. Identification of a plasma proteomic signature to distinguish pediatric osteosarcoma from benign osteochondroma. Proteomics6(11), 3426–3435 (2006).
  • Petricoin EF, Ardekani AM, Hitt BA et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet359(9306), 572–577 (2002).
  • Petricoin EF, Liotta LA. SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer. Curr. Opin. Biotechnol.15(1), 24–30 (2004).
  • Petricoin EF, Ornstein DK, Liotta LA. Clinical proteomics: applications for prostate cancer biomarker discovery and detection. Urol. Oncol.22(4), 322–328 (2004).
  • Petricoin EF III, Ornstein DK, Paweletz CP et al. Serum proteomic patterns for detection of prostate cancer. J. Natl Cancer Inst.94(20), 1576–1578 (2002).
  • Xiao Z, Prieto D, Conrads TP, Veenstra TD, Issaq HJ. Proteomic patterns: their potential for disease diagnosis. Mol. Cell. Endocrinol.230(1–2), 95–106 (2005).
  • Bjornstad A, Larsen BK, Skadsheim A, Jones MB, Andersen OK. The potential of ecotoxicoproteomics in environmental monitoring: biomarker profiling in mussel plasma using proteinchip array technology. J . Toxicol. Environ. Health A.69(1), 77–96 (2006).
  • Guerreiro N, Gomez-Mancilla B, Charmont S. Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid. Proteome Sci.4(1), 7 (2006).
  • Haubitz M, Wittke S, Weissinger EM et al. Urine protein patterns can serve as diagnostic tools in patients with IgA nephropathy. Kidney Int.67(6), 2313–2320 (2005).
  • Liao H, Wu J, Kuhn E et al. Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis. Arthritis Rheum.50(12), 3792–3803 (2004).
  • Poon TC, Hui AY, Chan HL et al. Prediction of liver fibrosis and cirrhosis in chronic hepatitis B infection by serum proteomic fingerprinting: a pilot study. Clin. Chem.51(2), 328–335 (2005).
  • Streckfus CF, Bigler LR, 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.35(5), 292–300 (2006).
  • Zhang Y, Wroblewski M, Hertz MI et al. Analysis of chronic lung transplant rejection by MALDI-TOF profiles of bronchoalveolar lavage fluid. Proteomics6(3), 1001–1010 (2006).
  • 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.97(4), 307–309 (2005).
  • Check E. Proteomics and cancer: running before we can walk? Nature429(6991), 496–497 (2004).
  • Diamandis EP. Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem.49(8), 1272–1275 (2003).
  • Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing data sets from different experiments. Bioinformatics (2004).
  • Hortin GL. The MALDI TOF Mass spectrometric view of the plasma proteome and peptidome. Clin. Chem.52(7), 1223-1237 (2006).
  • Fraser CG. Inherent biological variation and reference values. Clin. Chem. Lab. Med.42, 758–764 (2004).
  • Nelsestuen GL, Zhang Y, Martinez MB et al. Plasma protein profiling: unique and stable features of individuals. Proteomics5, 4012–4024 (2005).
  • Abdul-Salam VB, Paul GA, Ali JO et al. Identification of plasma protein biomarkers associated with idiopathic pulmonary arterial hypertension. Proteomics6(7), 2286–2294 (2006).
  • Stanley BA, Gundry RL, Cotter RJ, Van Eyk JE. Heart disease, clinical proteomics and mass spectrometry. Dis. Markers20(3), 167–178 (2004).
  • Bondarenko PV, Cockrill SL, Watkins LK, Cruzado ID, Macfarlane RD. Mass spectral study of polymorphism of the apolipoproteins of very low density lipoprotein. J. Lipid Res.40(3), 543–555 (1999).
  • Bergen HR III, Zeldenrust SR, Butz ML et al. Identification of transthyretin variants by sequential proteomic and genomic analysis. Clin. Chem.50(9), 1544–1552 (2004).
  • van der Poll T, van Deventer S. Endotoxemia in healthy subjects as a human model of inflammation. In: The Immune Response in the Critically Il. Cohen J (Ed.), Springer Verlag, Germany, 335–357 (1999)
  • Moore F. Complement Pier GB, Wetzler LM (Eds). ASM Press, WA, USA (2004).
  • Walport MJ. Complement. First of two parts. N. Engl. J. Med.344(14), 1058–1066 (2001).
  • Walport MJ. Complement. Second of two parts. N. Engl. J. Med.344(15), 1140–1144 (2001).
  • Kiernan UA, Tubbs KA, Nedelkov D, Niederkofler EE, Nelson RW. Detection of novel truncated forms of human serum amyloid A protein in human plasma. FEBS Lett.537(1–3), 166–170 (2003).
  • Ferrara JL, Levine JE. Graft-versus-host disease in the 21st century: new perspectives on an old problem. Semin. Hematol.43(1), 1–2 (2006).
  • Estenne M, Hertz MI. Bronchiolitis obliterans after human lung transplantation. Am. J. Respir. Crit. Care Med.166(4), 440–444 (2002).
  • Nelsestuen GL, Martinez MB, Hertz MI, Savik K, Wendt CH. Proteomic identification of human neutrophil alpha-defensins in chronic lung allograft rejection. Proteomics5, 1705–1713 (2005).
  • Thongboonkerd V, McLeish KR, Arthur JM, Klein JB. Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int.62(4), 1461–1469 (2002).
  • Pieper R, Gatlin CL, McGrath AM et al. Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics4(4), 1159–1174 (2004).
  • Thongboonkerd V, Malasit P. Renal and urinary proteomics: current applications and challenges. Proteomics5(4), 1033–1042 (2005).
  • Jurgens M, Appel A, Heine G et al. Towards characterization of the human urinary peptidome. Comb. Chem. High Throughput Screen.8(8), 757–765 (2005).
  • Celis JE, Wolf H, Ostergaard M. Bladder squamous cell carcinoma biomarkers derived from proteomics. Electrophoresis21(11), 2115–2121 (2000).
  • Sarto C, Deon C, Doro G et al. Contribution of proteomics to the molecular analysis of renal cell carcinoma with an emphasis on manganese superoxide dismutase. Proteomics1(10), 1288–1294 (2001).
  • Clarke W, Silverman BC, Zhang Z et al. Characterization of renal allograft rejection by urinary proteomic analysis. Ann. Surg.237(5), 660–665 (2003).
  • Schaub S, Rush D, Wilkins J et al. Proteomic-based detection of urine proteins associated with acute renal allograft rejection. J. Am. Soc. Nephrol.15(1), 219–227 (2004).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.