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


Authors: 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.; Variyath, A. M.; Wang, M.; Wang, P.; Whiteaker, J. R.; Zimmerman, L. J.; Carr, S. A.; Fisher, S. J.; Gibson, B. W.; Paulovich, A. G.; Regnier, F. E.; Rodriguez, H.; Spiegelman, C.; Tempst, P.; Liebler, D. C.; Stein, S. E.
Article Title: Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses
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.
Keywords: laboratories; proteome; reproducibility of results; animals; peptide; proteomics; saccharomyces cerevisiae; quantitative analysis; tandem mass spectrometry; saccharomyces cerevisiae proteins; chromatography, liquid; software; liquid chromatography; chickens; egg proteins; electrospray
Journal Title: Molecular & Cellular Proteomics
Volume: 9
Issue: 2
ISSN: 1535-9476
Publisher: Amer Soc Biochemistry Molecular Biology Inc  
Date Published: 2010-02-01
Start Page: 225
End Page: 241
Language: English
DOI: 10.1074/mcp.M900223-MCP200
PUBMED: 19837981
PROVIDER: scopus
PMCID: PMC2830836
DOI/URL:
Notes: --- - "Cited By (since 1996): 11" - "Export Date: 20 April 2011" - "CODEN: MCPOB" - "Source: Scopus"
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  1. Paul J Tempst
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