Research abstract

Analysis abstract

Nature Biotechnology 27, 633 - 641 (2009)
Published online: 28 June 2009 | Corrected online: 9 September 2009 | doi:10.1038/nbt.1546



There is a Corrigenda (September 2009) associated with this Analysis.

There is a Corrigenda (September 2009) associated with this Analysis.

There is a Corrigenda (September 2009) associated with this Analysis.

There is a Corrigenda (September 2009) associated with this Analysis.

There is a Corrigenda (September 2009) associated with this Analysis.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Terri A Addona1, Susan E Abbatiello1, Birgit Schilling2, Steven J Skates3, D R Mani1, David M Bunk4, Clifford H Spiegelman5, Lisa J Zimmerman6, Amy-Joan L Ham6, Hasmik Keshishian1, Steven C Hall7, Simon Allen7, Ronald K Blackman1,18, Christoph H Borchers8, Charles Buck9, Helene L Cardasis10, Michael P Cusack2, Nathan G Dodder4, Bradford W Gibson2, Jason M Held2, Tara Hiltke11, Angela Jackson8, Eric B Johansen7, Christopher R Kinsinger11, Jing Li6, Mehdi Mesri11, Thomas A Neubert10, Richard K Niles7, Trenton C Pulsipher3, David Ransohoff12, Henry Rodriguez11, Paul A Rudnick4, Derek Smith8, David L Tabb6, Tony J Tegeler13, Asokan M Variyath5, Lorenzo J Vega-Montoto5, Åsa Wahlander10, Sofia Waldemarson10, Mu Wang13,14, Jeffrey R Whiteaker15, Lei Zhao15, N Leigh Anderson16, Susan J Fisher7, Daniel C Liebler6, Amanda G Paulovich15, Fred E Regnier9, Paul Tempst17 & Steven A Carr1

Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low mug/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.

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  1. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
  2. Buck Institute for Age Research, Novato, California, USA.
  3. Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, USA.
  4. Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.
  5. Department of Statistics, Texas A&M University, College Station, Texas, USA.
  6. Vanderbilt University, Nashville, Tennessee, USA.
  7. Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA.
  8. University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia, Canada.
  9. Purdue University, West Lafayette, Indiana, USA.
  10. Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York, USA.
  11. National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
  12. University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA.
  13. Monarch Life Sciences, Indianapolis, Indiana, USA.
  14. Indiana University School of Medicine, Indianapolis, Indiana, USA.
  15. Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
  16. Plasma Proteome Institute, Washington DC, USA.
  17. Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
  18. Present address: Synta Pharmaceuticals, Lexington, Massachusetts, USA.

Correspondence to: Steven A Carr1 e-mail: scarr@broad.mit.edu

* In the version of this article initially published, the following acknowledgment was inadvertently left out: "The UCSF CPTAC team gratefully acknowledges the support of the Canary Foundation for providing funds to purchase a 4000 QTRAP mass spectrometer." The acknowlegment has been added to the HTML and PDF versions of the article.

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