Restructuring proteomics through verification

Biomarkers in Medicine

Volumn 4, Issue 6, 2010, Pages 799-803

  Boja, Emily ^a   Rivers, Robert ^a   Kinsinger, Christopher ^a   Mesri, Mehdi ^a   Hiltke, Tara ^a   Rahbar, Amir ^a   Rodriguez, Henry ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

biomarker; multiple reaction monitoring mass spectrometry; proteomics; verification

Indexed keywords

BIOLOGICAL MARKER;

BIOCHEMISTRY; CANCER RESEARCH; CLINICAL RESEARCH; CYTOLOGY; DIAGNOSTIC TEST APPROVAL; DIAGNOSTIC VALUE; ENZYME LINKED IMMUNOSORBENT ASSAY; FOOD AND DRUG ADMINISTRATION; HIGH THROUGHPUT SCREENING; HUMAN; MALIGNANT NEOPLASTIC DISEASE; MASS SPECTROMETRY; MICROFLUIDIC ANALYSIS; PERSONALIZED MEDICINE; PROTEIN ANALYSIS; PROTEIN MICROARRAY; PROTEIN PROCESSING; PROTEOMICS; REPRODUCIBILITY; REVIEW; SENSITIVITY AND SPECIFICITY; TRANSLATIONAL RESEARCH;

BIOLOGICAL MARKERS; HUMANS; MASS SPECTROMETRY; NATIONAL CANCER INSTITUTE (U.S.); PROTEOMICS; REPRODUCIBILITY OF RESULTS; UNITED STATES; UNITED STATES FOOD AND DRUG ADMINISTRATION;

EID: 78650732846     PISSN: 17520363     EISSN: None     Source Type: Journal    
DOI: 10.2217/bmm.10.92     Document Type: Review

References (30)

1. Etzioni R, Urban N, Ramsey S et al.: The case for early detection. Nat. Rev. Cancer 3, 243-252 (2003).
2. Feero WG, Guttmacher AE, Collins FS: Genomic medicine - an updated primer. N. Engl. J. Med. 362(21), 2001-2011 (2010).
3. Workman P: Strategies for treating cancers caused by multiple genome abnormalities: from concepts to cures? Curr. Opin. Investig. Drugs 4(12), 1410-1415 (2003).
4. Nibbe RK, Chance MR: Approaches to biomarkers in human colorectal cancer: looking back, to go forward. Biomark. Med. 3(4), 385-396 (2009).
5. Jolly Graham A, Potti A: Translating genomics into clinical practice: applications in lung cancer. Curr. Oncol. Rep. 11(4), 263-268 (2009).
6. Anderson L: Candidate-based proteomics in the search for biomarkers of cardiovascular disease. J. Physiol. 563, 23-60 (2005).
7. Rifai N, Gillette MA, Carr SA: Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983 (2006).
8. García-Foncillas J, Bandrés E, Zárate R, Remírez N: Proteomic analysis in cancer research: potential application in clinical use. Clin. Transl. Oncol. 8(4), 250-261 (2006).
9. Wang H, Wong CH, Chin A, Kennedy J, Zhang Q, Hanash S: Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS. J. Proteome Res. 8(12), 5412-5422 (2009).
10. Lee J, Soper SA, Murray KK: Microfuidic chips for mass spectrometry-based proteomics. J. Mass Spectrom. 44(5), 579-593 (2009).
11. Pierobon M, Calvert V, Belluco C et al.: Multiplexed cell signaling analysis of metastatic and nonmetastatic colorectal cancer reveals COX2-EGFR signaling activation as a potential prognostic pathway biomarker. Clin. Colorectal Cancer 8(2), 110-117 (2009).
12. Ramachandran N, Raphael JV, Hainsworth E et al.: Next-generation high-density self-assembling functional protein arrays. Nat. Methods 5(6), 535-538 (2008).
13. Beirne P, Pantelidis P, Charles P et al.: Multiplex immune serum biomarker profling in sarcoidosis and systemic sclerosis. Eur. Respir. J. 34(6), 1376-1382 (2009).
14. Kelleher MT, Fruhwirth G, Patel G et al.: The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients. Target Oncol. 4(3), 235-252 (2009).
15. Wang P, Whiteaker JR, Paulovich AG: The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol. Ther. 8(12), 1083-1094 (2009).
16. Gromov P, Gromova I, Bunkenborg J et al.: Up-regulated proteins in the fuid bathing the tumour cell microenvironment as potential serological markers for early detection of cancer of the breast. Mol. Oncol. 4(1), 65-89 (2010).
17. Levin Y, Schwarz E, Wang L, Leweke FM, Bahn S: Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples. J. Sep. Sci. 30(14), 2198-2203 (2007).
18. Neubert TA, Tempst P: Super SILAC for tumors and tissues. Nat. Methods 7(5), 361-362 (2010).
19. Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P: The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin. Appl. 2(10-11), 1386-1402 (2008).
20. Makawita S, Diamandis EP: The bottleneck in the cancer biomarker pipeline and protein quantifcation through mass spectrometry-based approaches: current strategies for candidate verifcation. Clin. Chem. 56(2), 212-222 (2010).
21. Anderson L, Hunter CL: Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5(4), 573-88 (2006).
22. Polanski M, Anderson NL: A list of candidate cancer biomarkers for targeted proteomics. Biomark. Insights 1, 1-48 (2007).
23. Backen AC, Cummings J, Mitchell C, Jayson G, Ward TH, Dive C: 'Fit-for-purpose' validation of SearchLight multiplex ELISAs of angiogenesis for clinical trial use. J. Immunol. Methods 342(1-2), 106-114 (2009).
24. Fu Q, Zhu J, Van Eyk JE: Comparison of multiplex immunoassay platforms. Clin. Chem. 56, 314-318 (2010).
25. Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW: Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome Res. 3(2), 235-244 (2004).
26. Kuhn E, Addona T, Keshishian H et al.: Developing multiplexed assays for troponin-I and interleukin-33 in plasma by peptide immunoaffnity enrichment and targeted mass spectrometry. Clin. Chem. 55(6), 1108-1117 (2009).
27. Hoofnagle AN, Becker JO, Wener MH, Heinecke JW: Quantifcation of thyroglobulin, a low-abundance serum protein, by immunoaffnity peptide enrichment and tandem mass spectrometry. Clin. Chem. 54(11), 1796-1804 (2008).
28. Addona TA, Abbatiello SE, Schilling B et al.: Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 27(7), 633-641 (2009).
29. Rodriguez H, Tezak Z, Mesri M et al.: Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin. Chem. 56(2), 237-243 (2010).
30. Regnier FE, Skates, SJ, Mesri M et al.: Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin. Chem. 56(2), 165-171 (2010).