Clinical proteomics: searching for better tumour markers with SELDI-TOF mass spectrometry

Banks, 2000, Proteomics: new perspectives, new biomedical opportunities, Lancet, 356, 1749, 10.1016/S0140-6736(00)03214-1 Bernhard, 2005, New insights into viral structure and virus-cell interactions through proteomics, Expert Rev Proteomics, 2, 577, 10.1586/14789450.2.4.577 Ho, 2005, From proteomics to biomarker discovery in Alzheimer's disease, Brain Res. Brain Res. Rev., 48, 360, 10.1016/j.brainresrev.2004.12.025 Anderson, 2005, Candidate-based proteomics in the search for biomarkers of cardiovascular disease, J. Physiol., 563, 23, 10.1113/jphysiol.2004.080473 Binz, 2003, Mass spectrometry-based proteomics: current status and potential use in clinical chemistry, Clin. Chem. Lab. Med., 41, 1540, 10.1515/CCLM.2003.237 MacBeath, 2002, Protein microarrays and proteomics, Nat. Genet., 32, 526, 10.1038/ng1037 Lopez, 2003, Protein micro- and macroarrays: digitizing the proteome, J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 787, 19, 10.1016/S1570-0232(02)00336-7 Lilley, 2002, Two-dimensional gel electrophoresis: recent advances in sample preparation, detection and quantitation, Curr. Opin. Chem. Biol., 6, 46, 10.1016/S1367-5931(01)00275-7 Heck, 2004, Mass spectrometry-based quantitative proteomics, Expert Rev. Proteomics, 1, 317, 10.1586/14789450.1.3.317 Schneider, 2005, Stable isotope methods for high-precision proteomics, Drug Discov. Today, 10, 353, 10.1016/S1359-6446(05)03381-7 Aebersold, 2003, Mass spectrometry-based proteomics, Nature, 422, 198, 10.1038/nature01511 Anderson, 2002, The human plasma proteome: history, character, and diagnostic prospects, Mol. Cell. Proteomics, 1, 845, 10.1074/mcp.R200007-MCP200 Hutchens, 1993, New desorption strategies for the mass spectrometric analysis of macromolecules, Rapid Commun. Mass Spectrom., 7, 576, 10.1002/rcm.1290070703 Caputo, 2003, Methods for on-chip protein analysis, Anal. Biochem., 321, 116, 10.1016/S0003-2697(03)00361-0 Petricoin, 2002, Use of proteomic patterns in serum to identify ovarian cancer, Lancet, 359, 572, 10.1016/S0140-6736(02)07746-2 Zhang, 2004, Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer, Cancer Res., 64, 5882, 10.1158/0008-5472.CAN-04-0746 Rai, 2002, Proteomic approaches to tumor marker discovery, Arch. Pathol. Lab. Med., 126, 1518, 10.5858/2002-126-1518-PATTMD Ye, 2003, Haptoglobin-α subunit as potential serum biomarker in ovarian cancer: identification and characterization using proteomic profiling and mass spectrometry, Clin. Cancer Res., 9, 2904 Kozak, 2003, Identification of biomarkers for ovarian cancer using strong anion-exchange ProteinChips: potential use in diagnosis and prognosis, Proc. Natl. Acad. Sci. U. S. A., 100, 12343, 10.1073/pnas.2033602100 Baggerly, 2004, Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments, Bioinformatics, 20, 777, 10.1093/bioinformatics/btg484 Diamandis, 2003, Point: Proteomic patterns in biological fluids: do they represent the future of cancer diagnostics?, Clin. Chem., 49, 1272, 10.1373/49.8.1272 Diamandis, 2005, Plasma protein profiling by mass spectrometry for cancer diagnosis: opportunities and limitations, Clin. Cancer Res., 11, 963, 10.1158/1078-0432.963.11.3 Baggerly, 2005, Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer, J. Natl. Cancer Inst., 97, 307, 10.1093/jnci/dji008 Sorace, 2003, A data review and re-assessment of ovarian cancer serum proteomic profiling, BMC Bioinformatics, 4, 24, 10.1186/1471-2105-4-24 Kozak, 2005, Characterization of serum biomarkers for detection of early stage ovarian cancer, Proteomics, 5, 4589, 10.1002/pmic.200500093 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 Van 't Veer, 2002, Gene expression profiling predicts clinical outcome of breast cancer, Nature, 415, 530, 10.1038/415530a Traub, 2005, SELDI-MS-based expression profiling of ductal invasive and lobular invasive human breast carcinomas, Pathol. Res. Pract., 201, 763, 10.1016/j.prp.2005.08.011 Pusztai, 2004, Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma, Cancer, 100, 1814, 10.1002/cncr.20203 Caputo, 2005, Peptide profiling in epithelial tumor plasma by the emerging proteomic techniques, J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 819, 59, 10.1016/j.jchromb.2005.01.022 Li, 2002, Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer, Clin. Chem., 48, 1296, 10.1093/clinchem/48.8.1296 Sauter, 2005, Proteomic analysis of nipple aspirate fluid using SELDI-TOF-MS, Int. J. Cancer, 114, 791, 10.1002/ijc.20742 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 Li, 2005, Identification of biomarkers for breast cancer in nipple aspiration and ductal lavage fluid, Clin. Cancer Res., 11, 8312, 10.1158/1078-0432.CCR-05-1538 Li, 2005, Independent validation of candidate breast cancer serum biomarkers identified by mass spectrometry, Clin. Chem., 51, 2229, 10.1373/clinchem.2005.052878 Mathelin, 2005, Serum biomarkers for detection of breast cancers: a prospective study, Breast Cancer Res. Treat Becker, 2004, Surfaced-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) differentiation of serum protein profiles of BRCA-1 and sporadic breast cancer, Ann. Surg. Oncol., 11, 907, 10.1245/ASO.2004.03.557 Heike, 2005, Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI ProteinChip system, Anticancer Res., 25, 1197 Linderholm, 2004, Protein profiles (proteomics) discriminating between relapses versus relapse-free survival after adjuvant tamoxifen in 272 patients with primary estrogen receptor (ER) and progesterone receptor (PgR) positive breast cancer, Proc. ASCO, 23, 859 Petricoin, 2002, Serum proteomic patterns for detection of prostate cancer, J. Natl. Cancer Inst., 94, 1576, 10.1093/jnci/94.20.1576 Qu, 2002, Boosted decision tree analysis of surface-enhanced laser desorption/ionization mass spectral serum profiles discriminates prostate cancer from noncancer patients, Clin. Chem., 48, 1835, 10.1093/clinchem/48.10.1835 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 Wagner, 2004, Computational protein biomarker prediction: a case study for prostate cancer, BMC Bioinformatics, 5, 26, 10.1186/1471-2105-5-26 Malik, 2005, Serum levels of an isoform of apolipoprotein A-II as a potential marker for prostate cancer, Clin. Cancer Res., 11, 1073, 10.1158/1078-0432.1073.11.3 Grizzle, 2003, Serum protein expression profiling for cancer detection: validation of a SELDI-based approach for prostate cancer, Dis. Markers, 19, 185, 10.1155/2004/546293 Semmes, 2005, Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility, Clin. Chem., 51, 102, 10.1373/clinchem.2004.038950 Chen, 2004, 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., 10, 8380, 10.1158/1078-0432.CCR-1162-03 Yu, 2004, An integrated approach to the detection of colorectal cancer utilizing proteomics and bioinformatics, World J. Gastroenterol., 10, 3127, 10.3748/wjg.v10.i21.3127 Engwegen, 2006, Identification of serum proteins discriminating colorectal cancer patients and healthy controls using surface enhanced laser desorption ionisation-time of flight mass spectrometry (SELDI-TOF MS), World J. Gastroenterol., 12, 1536, 10.3748/wjg.v12.i10.1536 Melle, 2005, Discovery and identification of α-defensins as low abundant, tumor-derived serum markers in colorectal cancer, Gastroenterology, 129, 66, 10.1053/j.gastro.2005.05.014 Albrethsen, 2005, Upregulated expression of human neutrophil peptides 1, 2 and 3 (HNP 1–3) in colon cancer serum and tumours: a biomarker study, BMC Cancer, 5, 8, 10.1186/1471-2407-5-8 Liotta, 2005, Importance of communication between producers and consumers of publicly available experimental data, J. Natl. Cancer Inst., 97, 310, 10.1093/jnci/dji053 Woong-Shick, 2005, Identification of hemoglobin-α and -β subunits as potential serum biomarkers for the diagnosis and prognosis of ovarian cancer, Cancer Sci., 96, 197, 10.1111/j.1349-7006.2005.00029.x Moshkovskii, 2005, Ovarian cancer marker of 11.7kDa detected by proteomics is a serum amyloid A1, Proteomics, 5, 3790, 10.1002/pmic.200401205 Le, 2005, Identification of serum amyloid A as a biomarker to distinguish prostate cancer patients with bone lesions, Clin. Chem., 51, 695, 10.1373/clinchem.2004.041087 Shiwa, 2003, 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., 309, 18, 10.1016/S0006-291X(03)01520-1 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 Tolson, 2004, Serum protein profiling by SELDI mass spectrometry: detection of multiple variants of serum amyloid α in renal cancer patients, Lab. Invest., 84, 845, 10.1038/labinvest.3700097 Rosty, 2002, Identification of hepatocarcinoma–intestine–pancreas/pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology, Cancer Res., 62, 1868 Wadsworth, 2004, Identification of patients with head and neck cancer using serum protein profiles, Arch. Otolaryngol. Head Neck Surg., 130, 98, 10.1001/archotol.130.1.98 Melle, 2003, Biomarker discovery and identification in laser microdissected head and neck squamous cell carcinoma with ProteinChip® technology, two-dimensional gel electrophoresis, tandem mass spectrometry, and immunohistochemistry, Mol. Cell. Proteomics, 2, 443, 10.1074/mcp.M300033-MCP200 Cho, 2004, Identification of serum amyloid A protein as a potentially useful biomarker to monitor relapse of nasopharyngeal cancer by serum proteomic profiling, Clin. Cancer Res., 10, 43, 10.1158/1078-0432.CCR-0413-3 Yang, 2004, Protein expression profiling of endometrial malignancies reveals a new tumor marker: chaperonin 10, J. Proteome Res., 3, 636, 10.1021/pr049975z Guo, 2005, A strategy for high-resolution protein identification in surface-enhanced laser desorption/ionization mass spectrometry: calgranulin A and chaperonin 10 as protein markers for endometrial carcinoma, Proteomics, 5, 1953, 10.1002/pmic.200401059 Lin, 2004, Application of SELDI-TOF mass spectrometry for the identification of differentially expressed proteins in transformed follicular lymphoma, Mod. Pathol., 17, 670, 10.1038/modpathol.3800100 Diamond, 2003, Use of ProteinChip™ array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin β-4, a differentially secreted protein from lymphoblastoid cell lines, J. Am. Soc. Mass Spectrom., 14, 760, 10.1016/S1044-0305(03)00265-4