Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses

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

doi:10.1074/mcp.M900223-MCP200

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses

Paul A. Rudnick, Karl R. Clauser, Lisa E. Kilpatrick, Dmitrii V. Tchekhovskoi, Pedatsur Neta, Nikša Blonder, Dean D. Billheimer, Ronald K. Blackman, David M. Bunk, Helene L. Cardasis, Amy Joan L. Ham, Jacob D. Jaffe, Christopher R. Kinsinger, Mehdi Mesri, Thomas A. Neubert, Birgit Schilling, David L. Tabb, Tony J. Tegeler, Lorenzo Vega-Montoto, Asokan Mulayath VariyathMu Wang, Pei Wang, Jeffrey R. Whiteaker, Lisa J. Zimmerman, Steven A. Carr, Susan J. Fisher, Bradford W. Gibson, Amanda G. Paulovich, Fred E. Regnier, Henry Rodriguez, Cliff Spiegelman, Paul Tempst, Daniel C. Liebler, Stephen E. Stein

Research output: Contribution to journal › Article › peer-review

168 Scopus citations

Abstract

A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.

Original language	English (US)
Pages (from-to)	225-241
Number of pages	17
Journal	Molecular and Cellular Proteomics
Volume	9
Issue number	2
DOIs	https://doi.org/10.1074/mcp.M900223-MCP200
State	Published - Feb 2010

ASJC Scopus subject areas

Analytical Chemistry
Biochemistry
Molecular Biology

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Rudnick, P. A., Clauser, K. R., Kilpatrick, L. E., Tchekhovskoi, D. V., Neta, P., Blonder, N., Billheimer, D. D., Blackman, R. K., Bunk, D. M., Cardasis, H. L., Ham, A. J. L., Jaffe, J. D., Kinsinger, C. R., Mesri, M., Neubert, T. A., Schilling, B., Tabb, D. L., Tegeler, T. J., Vega-Montoto, L., ... Stein, S. E. (2010). Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Molecular and Cellular Proteomics, 9(2), 225-241. https://doi.org/10.1074/mcp.M900223-MCP200

Rudnick, PA, Clauser, KR, Kilpatrick, LE, Tchekhovskoi, DV, Neta, P, Blonder, N, Billheimer, DD, Blackman, RK, Bunk, DM, Cardasis, HL, Ham, AJL, Jaffe, JD, Kinsinger, CR, Mesri, M, Neubert, TA, Schilling, B, Tabb, DL, Tegeler, TJ, Vega-Montoto, L, Variyath, AM, Wang, M, Wang, P, Whiteaker, JR, Zimmerman, LJ, Carr, SA, Fisher, SJ, Gibson, BW, Paulovich, AG, Regnier, FE, Rodriguez, H, Spiegelman, C, Tempst, P, Liebler, DC & Stein, SE 2010, 'Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses', Molecular and Cellular Proteomics, vol. 9, no. 2, pp. 225-241. https://doi.org/10.1074/mcp.M900223-MCP200

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abstract = "A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.",

author = "Rudnick, {Paul A.} and Clauser, {Karl R.} and Kilpatrick, {Lisa E.} and Tchekhovskoi, {Dmitrii V.} and Pedatsur Neta and Nik{\v s}a Blonder and Billheimer, {Dean D.} and Blackman, {Ronald K.} and Bunk, {David M.} and Cardasis, {Helene L.} and Ham, {Amy Joan L.} and Jaffe, {Jacob D.} and Kinsinger, {Christopher R.} and Mehdi Mesri and Neubert, {Thomas A.} and Birgit Schilling and Tabb, {David L.} and Tegeler, {Tony J.} and Lorenzo Vega-Montoto and Variyath, {Asokan Mulayath} and Mu Wang and Pei Wang and Whiteaker, {Jeffrey R.} and Zimmerman, {Lisa J.} and Carr, {Steven A.} and Fisher, {Susan J.} and Gibson, {Bradford W.} and Paulovich, {Amanda G.} and Regnier, {Fred E.} and Henry Rodriguez and Cliff Spiegelman and Paul Tempst and Liebler, {Daniel C.} and Stein, {Stephen E.}",

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AU - Tchekhovskoi, Dmitrii V.

AU - Neta, Pedatsur

AU - Blonder, Nikša

AU - Billheimer, Dean D.

AU - Blackman, Ronald K.

AU - Bunk, David M.

AU - Cardasis, Helene L.

AU - Ham, Amy Joan L.

AU - Jaffe, Jacob D.

AU - Kinsinger, Christopher R.

AU - Mesri, Mehdi

AU - Neubert, Thomas A.

AU - Schilling, Birgit

AU - Tabb, David L.

AU - Tegeler, Tony J.

AU - Vega-Montoto, Lorenzo

AU - Variyath, Asokan Mulayath

AU - Wang, Mu

AU - Wang, Pei

AU - Whiteaker, Jeffrey R.

AU - Zimmerman, Lisa J.

AU - Carr, Steven A.

AU - Fisher, Susan J.

AU - Gibson, Bradford W.

AU - Paulovich, Amanda G.

AU - Regnier, Fred E.

AU - Rodriguez, Henry

AU - Spiegelman, Cliff

AU - Tempst, Paul

AU - Liebler, Daniel C.

AU - Stein, Stephen E.

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Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses

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