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In 2006 the National Cancer Institute (NCI) established the 5-year Clinical Proteomics Technology Assessment for Cancer (CPTAC) program which aims to assess and improve measurement quality in clinical proteomics for cancer biomarker discovery and verification. NIST has been collaborating with the CPTAC program (including NCI as well as the 5 academic centers funded through CPTAC) in proteomic interlaboratory studies. Through these interlaboratory studies, NIST is identifying the major sources of variability in qualitative and quantitative proteomics. With these sources identified, NIST has developed computational tools to evaluate proteomic instrument performance and is also developing reference materials that can be used in concert with computational tools. Through this effort, NIST will deliver to the proteomics community methods and materials that can be used to evaluate measurement performance and proteomic data quality. The impact of this will be high quality, more confident proteomic data yielding, for clinical proteomics, more candidate biomarkers for clinical validation.
Additional Technical Details:
Participation in the CPTAC program and evaluation of the data from CPTAC interlaboratory studies has lead to the development at NIST of both proteomic data quality assessment tools and proteomic reference materials. The data assessment tools are based on the identification of more than 40 chromatographic and mass spectrometric instrument performance metrics. These metrics and their corresponding data tools are being used in the design of a certified reference material for “shotgun” proteomics.
Start Date:October 1, 2006
Lead Organizational Unit:mml
National Cancer Institute, Bethesda, MD
David M. Bunk
Related Programs and Projects:
Development of Reference Methods and Reference Materials for Proteins
Rudnick, P.A., Clauser, K.R., Kilpatrick, L.E., Tchekhovskoi, D.V., Neta, P., BillHeimer, D.D., Blackman, R.K., Bunk, D.M., Cardasis, H.L., Carr, S.A., Ham, A-J.L., Kinsinger, C.R., Neubert, T.A., Paulovich, A.G., Schilling, B., Spiegelman, C., Tabb, D.L., Tegler, T.J., Wang, M., Wang, P., Whiteaker, J.R., Zimmerman, L.J., Liebler, D.C., Stein, S.E., “Performance Metrics for Evaluating Liquid-Chromatography Tandem Mass Spectrometry Systems in Shotgun Proteomics” submitted to Nature Meth. (December 2008).
Tabb., D.L., Vega-Montoto, L., Variyath, A.M., Ham, A-J.L., Bunk, D.M., Kilpatrick, L.E., Rudnick, P.A., Cardasis, H., Clauser, K.R., Jaffe, J., Kowalski, K.A., Neubert, T.A., Tegeler, T.J., Wang, M., Whiteaker, J., Paulovich, A.G., Liebler, D.C., Spiegelman, C., “Reproducibility and Repeatability in CPTAC Consortium Proteomic Analyses by Liquid Chromatography-Tandem Mass Spectrometry” submitted to Nature Meth. (December 2008).
Paulovich, A.G., Billheimer, D., Ham, A-J. L., Vega-Montoto, L.J., Rudnick, P.A., Tabb, D.L., Wang, P., Blackman, R.K., Bunk, D.M., Cardasis, H., Clauser, K.R., Kinsinger, C.R., Schilling, B., Tegeler, T.J., Variyath, A.M., Wang, M., Whiteaker, J.R., Zimmerman, L.J., Carr, S.A., Fisher, S.J., Gibson, B.W., Mesri, M., Neubert, T.A., Regnier, F.E., Rodriguez, H., Spiegelman, C., Stein, S.E., Tempst, P., Liebler, D.C., “A Reference Yeast Proteome for Benchmarking LC-MS Platform Performance” submitted to Nature Meth. (December 2008).
Addona, T., Abbatiello, S.E., Schilling, B., Skates, S.J., Mani, D.R., Bunk, D. M., Spiegelman, C.H., Zimmerman, L.J., Ham, A-J.L., Keshishian, H., Hall, S.C., Allen, S., Blackman, R.K., Borchers, C.H., Buck, C., Cardasis, H.L., Cusack, M.P., Dodder, N.G., Gibson, B.W., Held, J.M., Hiltke, T., Jackson, A., Johansen, E.B., Kinsinger, C.R., Li, J., Mesri, M., Neubert, T.A., Niles, R.K., Pulsipher, T.C., Rodriguez, H., Rudnick, P.A., Smith, D., Tabb, D.L., Tegeler, T.J., Variyath, A.M., Vega-Montoto, L.J., Wahlander, A., Waldemarson, S., Wang, M., Whiteaker, J.R.; Zhao, L., Anderson, N.L., Fisher, S.J., Liebler, D.C., Paulovich, A.G., Regneir, F.E., Tempst, P., Carr, S.A., “A Multi-site Assessment of Precision and Reproducibility of Multiple Reaction Monintoring-based Measurements:
Toward Quantitative Protein Biomarker Verification in Human Plasma” submitted to Nature Biotech. (January 2009).