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Mol Cell Proteomics DOI:10.1074/mcp.M900223-MCP200

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

Publication TypeJournal Article
Year of Publication2010
AuthorsRudnick, PA, Clauser, KR, Kilpatrick, LE, Tchekhovskoi, DV, Neta, P, Blonder, N, Billheimer, DD, Blackman, RK, Bunk, DM, Cardasis, HL, Ham, A-JL, Jaffe, JD, Kinsinger, CR, Mesri, M, Neubert, TA, Schilling, B, Tabb, DL, Tegeler, TJ, Vega-Montoto, L, Variyath, AMulayath, 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
JournalMol Cell Proteomics
Date Published2010 Feb
KeywordsAnimals, Chickens, Chromatography, Liquid, Egg Proteins, Laboratories, Proteome, Proteomics, Reproducibility of Results, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Software, Tandem Mass Spectrometry

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.


Alternate JournalMol. Cell Proteomics
PubMed ID19837981
PubMed Central IDPMC2830836
Grant ListU24CA126480 / CA / NCI NIH HHS / United States
U24CA126477 / CA / NCI NIH HHS / United States
U24 CA126485 / CA / NCI NIH HHS / United States
U24CA126476 / CA / NCI NIH HHS / United States
U24 CA126480 / CA / NCI NIH HHS / United States
U24 CA126477 / CA / NCI NIH HHS / United States
U24 CA126479 / CA / NCI NIH HHS / United States
U24 CA126476 / CA / NCI NIH HHS / United States
U24CA126485 / CA / NCI NIH HHS / United States
U24CA126479 / CA / NCI NIH HHS / United States