Accurate inclusion mass screening: A bridge from unbiased discovery to targeted assay development for biomarker verification

Molecular and Cellular Proteomics

Volumn 7, Issue 10, 2008, Pages 1952-1962

  Jaffe, Jacob D ^a   Keshishian, Hasmik ^a   Chang, Betty ^a   Addona, Theresa A ^a   Gilette, Michael A ^a   Carr, Steven A ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE REDUCTASE; BETAINE HOMOCYSTEINE METHYLTRANSFERASE; BIOLOGICAL MARKER; CALRETICULIN; PHOSPHOPROTEIN PHOSPHATASE; PHOSPHOPROTEIN PHOSPHATASE 1G; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DISEASE MARKER; FEMALE; HUMAN; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MASS SCREENING; PRIORITY JOURNAL; PROTEIN BLOOD LEVEL; PROTEIN DETERMINATION; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY;

BIOLOGICAL ASSAY; BIOLOGICAL MARKERS; DATABASES, PROTEIN; FEMALE; HUMANS; MASS SCREENING; PEPTIDES; PILOT PROJECTS; REPRODUCIBILITY OF RESULTS;

EID: 55049104915     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800218-MCP200     Document Type: Article

References (16)

1. Etzioni, R., Urban, N., Ramsey, S., McIntosh, M., Schwartz, S., Reid, B., Radich, J., Anderson, G., and Hartwell, L. (2003) The case for early detection. Nat. Rev. Cancer 3, 243-252
2. Anderson, N. L., and Anderson, N. G. (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1, 845-867
3. Anderson, N. L. (2005) The roles of multiple proteomic platforms in a pipeline for new diagnostics. Mol. Cell. Proteomics 4,1 441-1444
4. Gutman, S., and Kessler, L. G. (2006) The US Food and Drug Administration perspective on cancer biomarker development. Nat. Rev. Cancer 6, 565-571
5. Rifai, N., Gillette, M. A., and Carr, S. A. (2006) Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983
6. Gortzak-Uzan, L., Ignatchenko, A., Evangelou, A. I., Agochiya, M., Brown, K. A., St Onge, P., Kireeva, I., Schmitt-Ulms, G., Brown, T. J., Murphy, J., Rosen, B., Shaw, P., Jurisica, I., and Kislinger, T. (2008) A proteome resource of ovarian cancer ascites: integrated proteomic and bioinformatic analyses to identify putative biomarkers. J. Proteome Res. 7, 339-351
7. Paulovich, A. G., Whiteaker, J. R., Hoofnagle, A. N., and Wang, P. (2008) The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin. Appl., in press
8. Keshishian, H., Addona, T., Burgess, M., Kuhn, E., and Carr, S. A. (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 6, 2212-2229
9. Whiteaker, J. R., Zhang, H., Zhao, L., Wang, P., Kelly-Spraft, K. S., Ivey, R. G., Piening, B. D., Feng, L. C., Kasarda, E., Gurley, K. E., Eng, J. K., Chodosh, L. A., Kemp, C. J., McIntosh, M. W., and Paulovich, A. G. (2007) Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J. Proteome Res. 6, 3962-3975
10. Calvo, S., Jain, M., Xie, X., Sheth, S. A., Chang, B., Goldberger, O. A., Spinazzola, A., Zeviani, M., Carr, S. A., and Mootha, V. K. (2006) Systematic identification of human mitochondrial disease genes through integrative genomics. Nat. Genet. 38, 576-582
11. Jaffe, J. D., Mani, D. R., Leptos, K. C., Church, G. M., Gillette, M. A., and Carr, S. A. (2006) PEPPeR, a platform for experimental proteomic pattern recognition. Mol. Cell. Proteomics 5, 1927-1941
12. Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., and Pearson, T. W. (2004) Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome Res. 3, 235-244
13. Berna, M., Ott, L., Engle, S., Watson, D., Solter, P., and Ackermann, B. (2008) Quantification of NTproBNP in rat serum using immunoprecipitation and LC/MS/MS: a biomarker of drug-induced cardiac hypertrophy. Anal. Chem. 80, 561-566
14. Whiteaker, J. R., Zhao, L., Zhang, H. Y., Fang, L. C., Piening, B. D., Anderson, L., and Paulovich, A. G. (2007) Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal. Biochem. 362, 44-54
15. Picotti, P., Aebersold, R., and Domon, B. (2007) The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics 6, 1589-1598
16. Unwin, R. D., Griffiths, J. R., Leverentz, M. K., Grallert, A., Hagan, I. M., and Whetton, A. D. (2005) Multiple reaction monitoring to identify sites of protein phosphorylation with high sensitivity. Mol. Cell. Proteomics 4, 1134-1144