Scientific Publications

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

Publication TypeJournal Article
AuthorsRudnick, PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P., Blonder N., Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, 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, and Stein SE
AbstractA 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.
Year of Publication2010
JournalMolecular & cellular proteomics : MCP
Volume9
Issue2
Pages225-41
Date Published (YYYY/MM/DD)2010/02/01
ISSN Number1535-9476
DOI10.1074/mcp.M900223-MCP200
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/19837981?dopt=Abstract