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 journalArticlepeer-review

160 Scopus citations


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 languageEnglish (US)
Pages (from-to)225-241
Number of pages17
JournalMolecular and Cellular Proteomics
Issue number2
StatePublished - Feb 2010

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology


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