TY - JOUR
T1 - Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses
AU - Rudnick, Paul A.
AU - Clauser, Karl R.
AU - Kilpatrick, Lisa E.
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.
PY - 2010/2
Y1 - 2010/2
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=76749122411&partnerID=8YFLogxK
U2 - 10.1074/mcp.M900223-MCP200
DO - 10.1074/mcp.M900223-MCP200
M3 - Article
C2 - 19837981
AN - SCOPUS:76749122411
SN - 1535-9476
VL - 9
SP - 225
EP - 241
JO - Molecular and Cellular Proteomics
JF - Molecular and Cellular Proteomics
IS - 2
ER -