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A Multi-site Assessment of Precision and Reproducibility of Multiple Reaction Monitoring-based Measurements: Toward Quantitative Protein Biomarker Verification in Human Plasma



Nathan G. Dodder, Terri Addona, Susan Abbatiello, Birgit Schilling, Steven Skates, D.R. Mani, David M. Bunk, Clifford Spiegelman, Lisa Zimmerman, Amy-Joan Ham, Hasmik Keshishian, Steven Hall, Simon Allen, Ronald Blackman, Christoph Borchers, Charles Buck, Helene Cardasis, Michael Cusack, Bradford Gibson, Jason Held, Tara Hiltke, Angela Jackson, Eric Johansen, Christopher Kinsinger, Jing Li, Mehdi Mesri, Thomas Neubert, Richard Niles, Trenton Pulsipher, Henry Rodriguez, Paul A. Rudnick, Derek Smith, David Tabb, Tony Tegeler, Henry Variyath, Lorenzo Vega-Montoto, Asa Wahlander, Sofia Waldemarson, Mu Wang, Jeffrey Whitaker, Lei Zhao, N. Leigh Anderson, Susan Fisher, Daniel Liebler, Amanda Paulovich, Fred Regnier, Paul Tempst, Steven Carr


Candidate-based biomarker verification relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the biomarker discovery pipeline that bridges unbiased discovery to pre-clinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry has suitable assay performance for quantitative measurements of candidate protein biomarkers in plasma, reproducibility and transferability of these assays across the biomarker community has not been demonstrated. Here we describe a multi-laboratory study to assess performance metrics of multiplexed, MRM-based assays, including reproducibility, recovery, and limits of detection and quantitation. Using common materials and standardized protocols, we demonstrate that MS-based assays of proteins in plasma can be sensitive and highly reproducible across laboratories and instrument platforms. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.
Nature Biotechnology


proteomics, NCI, CPTAC, LC/MS/MS, quantification


Dodder, N. , Addona, T. , Abbatiello, S. , Schilling, B. , , S. , Mani, D. , Bunk, D. , Spiegelman, C. , Zimmerman, L. , Ham, A. , Keshishian, H. , Hall, S. , Allen, S. , Blackman, R. , Borchers, C. , Buck, C. , Cardasis, H. , Cusack, M. , Gibson, B. , Held, J. , Hiltke, T. , Jackson, A. , Johansen, E. , Kinsinger, C. , Li, J. , Mesri, M. , Neubert, T. , Niles, R. , Pulsipher, T. , Rodriguez, H. , Rudnick, P. , Smith, D. , Tabb, D. , Tegeler, T. , Variyath, H. , Vega-Montoto, L. , Wahlander, A. , Waldemarson, S. , Wang, M. , Whitaker, J. , Zhao, L. , , N. , Fisher, S. , Liebler, D. , Paulovich, A. , Regnier, F. , Tempst, P. and Carr, S. (2009), A Multi-site Assessment of Precision and Reproducibility of Multiple Reaction Monitoring-based Measurements: Toward Quantitative Protein Biomarker Verification in Human Plasma, Nature Biotechnology, [online], (Accessed May 25, 2024)


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Created June 28, 2009, Updated February 19, 2017