The ongoing evolution of proteomics in malignancy

Collins, 2003, A vision for the future of genomics research, Nature, 422, 835, 10.1038/nature01626 Zhao, 2004, An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays, Cancer Res., 64, 3060, 10.1158/0008-5472.CAN-03-3308 Pollack, 1999, Genome-wide analysis of DNA copy-number changes using cDNA microarrays, Nat. Genet., 23, 41, 10.1038/14385 Posadas, 2007, A phase II and pharmacodynamic study of gefitinib in patients with refractory or recurrent epithelial ovarian cancer, Cancer, 109, 1323, 10.1002/cncr.22545 Azad, 2006, Proteomics in clinical trials and practice: present uses and future promise, Mol. Cell Proteomics, 5, 1819, 10.1074/mcp.R600008-MCP200 Becker, 2006, Clinical proteomics: new trends for protein microarrays, Curr. Med. Chem., 13, 1831, 10.2174/092986706777452506 Becker, 2007, Quantitative protein analysis from formalin-fixed tissues: implications for translational clinical research and nanoscale molecular diagnosis, J. Pathol., 211, 370, 10.1002/path.2107 Emmert-Buck, 1996, Laser capture microdissection, Science, 274, 998, 10.1126/science.274.5289.998 Fuller, 2003, Laser capture microdissection and advanced molecular analysis of human breast cancer, J. Mammary Gland Biol. Neoplasia, 8, 335, 10.1023/B:JOMG.0000010033.49464.0c O’Farrell, 1975, High resolution two-dimensional electrophoresis of proteins, J. Biol. Chem., 250, 4007, 10.1016/S0021-9258(19)41496-8 Van den Bergh, 2005, Recent advances in 2D electrophoresis: an array of possibilities, Expert Rev. Proteomics, 2, 243, 10.1586/14789450.2.2.243 Bjellqvist, 1982, Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications, J. Biochem. Biophys. Methods, 6, 317, 10.1016/0165-022X(82)90013-6 Von Eggeling, 2001, Fluorescent dual colour 2D-protein gel electrophoresis for rapid detection of differences in protein pattern with standard image analysis software, Int. J. Mol. Med., 8, 373 Lilley, 2004, All about DIGE: quantification technology for differential-display 2D-gel proteomics, Expert Rev. Proteomics, 1, 401, 10.1586/14789450.1.4.401 Domon, 2006, Mass spectrometry and protein analysis, Science, 312, 212, 10.1126/science.1124619 Krueger, 2006, Posttranslational protein modifications: current implications for cancer detection, prevention, and therapeutics, Mol. Cell Proteomics, 5, 1799, 10.1074/mcp.R600009-MCP200 Qian, 2006, Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications, Mol. Cell Proteomics, 5, 1727, 10.1074/mcp.M600162-MCP200 Hortin, 2006, The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome, Clin. Chem., 52, 1223, 10.1373/clinchem.2006.069252 Seibert, 2005, Advances in clinical cancer proteomics: SELDI-ToF-mass spectrometry and biomarker discovery, Brief Funct. Genomic Proteomic, 4, 16, 10.1093/bfgp/4.1.16 Engwegen, 2006, Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry, Trends Pharmacol. Sci., 27, 251, 10.1016/j.tips.2006.03.003 Poon, 2007, Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices, Expert Rev. Proteomics, 4, 51, 10.1586/14789450.4.1.51 Petricoin, 2006, The blood peptidome: a higher dimension of information content for cancer biomarker discovery, Nat. Rev. Cancer, 6, 961, 10.1038/nrc2011 Fountoulakis, 2004, Depletion of the high-abundance plasma proteins, Amino Acids, 27, 249, 10.1007/s00726-004-0141-1 Zhou, 2004, An investigation into the human serum “interactome”, Electrophoresis, 25, 1289, 10.1002/elps.200405866 Terracciano, 2006, Selective binding and enrichment for low-molecular weight biomarker molecules in human plasma after exposure to nanoporous silica particles, Proteomics, 6, 3243, 10.1002/pmic.200500614 Ahn, 2007, Achieving in-depth proteomics profiling by mass spectrometry, ACS Chem. Biol., 2, 39, 10.1021/cb600357d Wagner, 2004, Challenges for biomarkers in cancer detection, Ann. N.Y. Acad. Sci., 1022, 9, 10.1196/annals.1318.003 Bradford, 2006, Molecular markers of prostate cancer, Urol. Oncol., 24, 538, 10.1016/j.urolonc.2006.07.004 Rustin, 2006, Comparison of CA-125 and standard definitions of progression of ovarian cancer in the intergroup trial of cisplatin and paclitaxel versus cisplatin and cyclophosphamide, J. Clin. Oncol., 24, 45, 10.1200/JCO.2005.01.2757 Petricoin, 2002, Use of proteomic patterns in serum to identify ovarian cancer, Lancet, 359, 572, 10.1016/S0140-6736(02)07746-2 Petricoin, 2002, Serum proteomic patterns for detection of prostate cancer, J. Natl. Cancer Inst., 94, 1576, 10.1093/jnci/94.20.1576 Agranoff, 2006, Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum, Lancet, 368, 1012, 10.1016/S0140-6736(06)69342-2 Goncalves, 2006, Postoperative serum proteomic profiles may predict metastatic relapse in high-risk primary breast cancer patients receiving adjuvant chemotherapy, Oncogene, 25, 981, 10.1038/sj.onc.1209131 Diamandis, 2006, Serum proteomic profiling by matrix-assisted laser desorption–ionization time-of-flight mass spectrometry for cancer diagnosis: next steps, Cancer Res., 66, 5540, 10.1158/0008-5472.CAN-05-4503 Diamandis, 2004, Proteomic patterns to identify ovarian cancer: 3 years on, Expert Rev. Mol. Diagn., 4, 575, 10.1586/14737159.4.5.575 Anderson, 2002, The human plasma proteome: history, character, and diagnostic prospects, Mol. Cell Proteomics, 1, 845, 10.1074/mcp.R200007-MCP200 Omenn, 2005, Exploring the human plasma proteome, Proteomics, 5, 3223, 10.1002/pmic.200590056 Omenn, 2005, Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database, Proteomics, 5, 3226, 10.1002/pmic.200500358 States, 2006, Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study, Nat. Biotechnol., 24, 333, 10.1038/nbt1183 Fung, 2005, Classification of cancer types by measuring variants of host response proteins using SELDI serum assays, Int. J. Cancer, 115, 783, 10.1002/ijc.20928 Koopmann, 2004, Serum diagnosis of pancreatic adenocarcinoma using surface-enhanced laser desorption and ionization mass spectrometry, Clin. Cancer Res., 10, 860, 10.1158/1078-0432.CCR-1167-3 Yang, 2005, Application of serum SELDI proteomic patterns in diagnosis of lung cancer, BMC Cancer, 5, 83, 10.1186/1471-2407-5-83 Paradis, 2005, Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases, Hepatology, 41, 40, 10.1002/hep.20505 Adam, 2002, Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men, Cancer Res., 62, 3609 Ornstein, 2004, Serum proteomic profiling can discriminate prostate cancer from benign prostates in men with total prostate specific antigen levels between 2.5 and 15.0ng/ml, J. Urol., 172, 1302, 10.1097/01.ju.0000139572.88463.39 Wang, 2005, Autoantibody signatures in prostate cancer, N Engl J Med, 353, 1224, 10.1056/NEJMoa051931 Cho-Chung, 2006, Autoantibody biomarkers in the detection of cancer, Biochim. Biophys. Acta, 1762, 587, 10.1016/j.bbadis.2006.04.001 Ricolleau, 2006, Surface-enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors, Proteomics, 6, 1963, 10.1002/pmic.200500283 Mor, 2005, Serum protein markers for early detection of ovarian cancer, Proc. Natl. Acad. Sci. U.S.A., 102, 7677, 10.1073/pnas.0502178102 Nedelkov, 2006, Mass spectrometry-based immunoassays for the next phase of clinical applications, Expert Rev. Proteomics, 3, 631, 10.1586/14789450.3.6.631 Pisitkun, 2006, Discovery of urinary biomarkers, Mol. Cell Proteomics, 5, 1760, 10.1074/mcp.R600004-MCP200 Downes, 2006, Application of proteomic strategies to the identification of urinary biomarkers for prostate cancer: a review, Biomarkers, 11, 406, 10.1080/13547500600799821 Downes, 2006, Urinary markers for prostate cancer, BJU Int. Zerefos, 2006, Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE, Proteomics, 6, 4346, 10.1002/pmic.200500671 Pieper, 2004, 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, Proteomics, 4, 1159, 10.1002/pmic.200300661 Theodorescu, 2006, Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis, Lancet Oncol., 7, 230, 10.1016/S1470-2045(06)70584-8 Khwaja, 2006, Proteomic analysis of cerebrospinal fluid discriminates malignant and nonmalignant disease of the central nervous system and identifies specific protein markers, Proteomics, 6, 6277, 10.1002/pmic.200600135 Romeo, 2005, CSF proteome: a protein repository for potential biomarker identification, Expert Rev. Proteomics, 2, 57, 10.1586/14789450.2.1.57 Magi, 2006, Proteome analysis of bronchoalveolar lavage in lung diseases, Proteomics, 6, 6354, 10.1002/pmic.200600303 Liao, 2004, 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, 3792, 10.1002/art.20720 Ruetschi, 2005, Proteomic analysis using protein chips to detect biomarkers in cervical and amniotic fluid in women with intra-amniotic inflammation, J. Proteome Res., 4, 2236, 10.1021/pr050139e Nicholas, 2006, Shotgun proteomic analysis of human-induced sputum, Proteomics, 6, 4390, 10.1002/pmic.200600011 Pawlik, 2005, Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry, Breast Cancer Res. Treat., 89, 149, 10.1007/s10549-004-1710-4 Cappuzzo, 2005, Epidermal growth factor receptor gene and protein and gefitinib sensitivity in non-small-cell lung cancer, J. Natl. Cancer Inst., 97, 643, 10.1093/jnci/dji112 Okamoto, 2006, Comparative proteomic profiles of meningioma subtypes, Cancer Res., 66, 10199, 10.1158/0008-5472.CAN-06-0955 Jacquemier, 2005, Protein expression profiling identifies subclasses of breast cancer and predicts prognosis, Cancer Res., 65, 767, 10.1158/0008-5472.767.65.3 Rakha, 2007, Prognostic markers in triple-negative breast cancer, Cancer, 109, 25, 10.1002/cncr.22381 Yanagisawa, 2003, Proteomic patterns of tumour subsets in non-small-cell lung cancer, Lancet, 362, 433, 10.1016/S0140-6736(03)14068-8 Clarke, 2003, Characterization of renal allograft rejection by urinary proteomic analysis, Ann. Surg., 237, 660, 10.1097/01.SLA.0000064293.57770.42 Posadas, 2004, A phase II clinical trial with proteomic profiling of imatinib mesylate in patients with refractory or relapsed epithelial ovarian cancer (EOC) Xiao, 2004, Serum proteomic profiles suggest celecoxib-modulated targets and response predictors, Cancer Res., 64, 2904, 10.1158/0008-5472.CAN-03-3754 Okano, 2007, Proteomic signature corresponding to the response to gefitinib (Iressa, ZD1839), an epidermal growth factor receptor tyrosine kinase inhibitor in lung adenocarcinoma, Clin. Cancer Res., 13, 799, 10.1158/1078-0432.CCR-06-1654 Hirsch, 2003, Epidermal growth factor receptor in non-small-cell lung carcinomas: correlation between gene copy number and protein expression and impact on prognosis, J. Clin. Oncol., 21, 3798, 10.1200/JCO.2003.11.069 Kakiuchi, 2004, Prediction of sensitivity of advanced non-small cell lung cancers to gefitinib (Iressa, ZD1839), Hum. Mol. Genet., 13, 3029, 10.1093/hmg/ddh331