Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance

Amanda G. Paulovich, David D Billheimer, Amy Joan L Ham, Lorenzo Vega-Montoto, Paul A. Rudnick, David L. Tabb, Pei Wang, Ronald K. Blackman, David M. Bunk, Helene L. Cardasis, Karl R. Clauser, Christopher R. Kinsinger, Birgit Schilling, Tony J. Tegeler, Asokan Mulayath Variyath, Mu Wang, Jeffrey R. Whiteaker, Lisa J. Zimmerman, David Fenyo, Steven A. Carr & 10 others Susan J. Fisher, Bradford W. Gibson, Mehdi Mesri, Thomas A. Neubert, Fred E. Regnier, Henry Rodriguez, Cliff Spiegelman, Stephen E. Stein, Paul Tempst, Daniel C. Liebler

Research output: Contribution to journalArticle

122 Citations (Scopus)

Abstract

Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize preanalytical and analytical variation in comparative proteomics experiments.

Original languageEnglish (US)
Pages (from-to)242-254
Number of pages13
JournalMolecular and Cellular Proteomics
Volume9
Issue number2
DOIs
StatePublished - Feb 2010

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Benchmarking
Proteome
Yeast
Yeasts
Proteomics
Technology
Proteins
Quality Control
Saccharomyces cerevisiae
Quality control
Ions

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Analytical Chemistry

Cite this

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. / Paulovich, Amanda G.; Billheimer, David D; Ham, Amy Joan L; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Tabb, David L.; Wang, Pei; Blackman, Ronald K.; Bunk, David M.; Cardasis, Helene L.; Clauser, Karl R.; Kinsinger, Christopher R.; Schilling, Birgit; Tegeler, Tony J.; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fenyo, David; Carr, Steven A.; Fisher, Susan J.; Gibson, Bradford W.; Mesri, Mehdi; Neubert, Thomas A.; Regnier, Fred E.; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E.; Tempst, Paul; Liebler, Daniel C.

In: Molecular and Cellular Proteomics, Vol. 9, No. 2, 02.2010, p. 242-254.

Research output: Contribution to journalArticle

Paulovich, AG, Billheimer, DD, Ham, AJL, Vega-Montoto, L, Rudnick, PA, Tabb, DL, Wang, P, Blackman, RK, Bunk, DM, Cardasis, HL, Clauser, KR, Kinsinger, CR, Schilling, B, Tegeler, TJ, Variyath, AM, Wang, M, Whiteaker, JR, Zimmerman, LJ, Fenyo, D, Carr, SA, Fisher, SJ, Gibson, BW, Mesri, M, Neubert, TA, Regnier, FE, Rodriguez, H, Spiegelman, C, Stein, SE, Tempst, P & Liebler, DC 2010, 'Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance', Molecular and Cellular Proteomics, vol. 9, no. 2, pp. 242-254. https://doi.org/10.1074/mcp.M900222-MCP200
Paulovich, Amanda G. ; Billheimer, David D ; Ham, Amy Joan L ; Vega-Montoto, Lorenzo ; Rudnick, Paul A. ; Tabb, David L. ; Wang, Pei ; Blackman, Ronald K. ; Bunk, David M. ; Cardasis, Helene L. ; Clauser, Karl R. ; Kinsinger, Christopher R. ; Schilling, Birgit ; Tegeler, Tony J. ; Variyath, Asokan Mulayath ; Wang, Mu ; Whiteaker, Jeffrey R. ; Zimmerman, Lisa J. ; Fenyo, David ; Carr, Steven A. ; Fisher, Susan J. ; Gibson, Bradford W. ; Mesri, Mehdi ; Neubert, Thomas A. ; Regnier, Fred E. ; Rodriguez, Henry ; Spiegelman, Cliff ; Stein, Stephen E. ; Tempst, Paul ; Liebler, Daniel C. / Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. In: Molecular and Cellular Proteomics. 2010 ; Vol. 9, No. 2. pp. 242-254.
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