Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses

被引：154

作者：

Rudnick, Paul A. ^{[2
]}

Clauser, Karl R. ^{[3
]}

Kilpatrick, Lisa E. ^{[4
]}

Tchekhovskoi, Dmitrii V. ^{[2
]}

Neta, Pedatsur ^{[2
]}

Blonder, Niksa ^{[2
]}

Billheimer, Dean D. ^{[5
]}

Blackman, Ronald K. ^{[3
]}

Bunk, David M. ^{[4
]}

Cardasis, Helene L. ^{[6
]}

Ham, Amy-Joan L. ^{[1
]}

Jaffe, Jacob D. ^{[3
]}

Kinsinger, Christopher R. ^{[7
]}

Mesri, Mehdi ^{[7
]}

Neubert, Thomas A. ^{[6
]}

Schilling, Birgit ^{[8
]}

Tabb, David L. ^{[1
]}

Tegeler, Tony J. ^{[9
]}

Vega-Montoto, Lorenzo ^{[10
]}

Variyath, Asokan Mulayath ^{[10
]}

Wang, Mu ^{[9
]}

Wang, Pei ^{[11
]}

Whiteaker, Jeffrey R. ^{[11
]}

Zimmerman, Lisa J. ^{[1
]}

Carr, Steven A. ^{[1
]}

Fisher, Susan J. ^{[12
]}

Gibson, Bradford W. ^{[8
]}

Paulovich, Amanda G. ^{[11
]}

Regnier, Fred E. ^{[13
]}

Rodriguez, Henry ^{[7
]}

Spiegelman, Cliff ^{[10
]}

Tempst, Paul ^{[14
]}

Liebler, Daniel C. ^{[1
]}

Stein, Stephen E. ^{[2
]}

机构：

[1] Vanderbilt Univ, Sch Med, Nashville, TN 37232 USA

[2] NIST, Gaithersburg, MD 20899 USA

[3] MIT & Harvard, Broad Inst, Cambridge, MA 02141 USA

[4] NIST, Hollings Marine Lab, Charleston, SC 29412 USA

[5] Univ Arizona, Tucson, AZ 85721 USA

[6] NYU, Skirball Inst, New York, NY 10016 USA

[7] NCI, NIH, Bethesda, MD 20892 USA

[8] Buck Inst Age Res, Novato, CA 94945 USA

[9] Monarch Life Sci, Indianapolis, IN 46202 USA

[10] Texas A&M Univ, College Stn, TX 77843 USA

[11] Fred Hutchinson Canc Res Ctr, Seattle, WA 98109 USA

[12] Univ Calif San Francisco, San Francisco, CA 94143 USA

[13] Purdue Univ, Bindley Biosci Ctr, W Lafayette, IN 47907 USA

[14] Mem Sloan Kettering Canc Ctr, New York, NY 10065 USA

来源：

MOLECULAR & CELLULAR PROTEOMICS | 2010年 / 9卷 / 02期

基金：

美国国家卫生研究院;

关键词：

PEPTIDE IDENTIFICATION; PROTEIN-ABUNDANCE;

D O I：

10.1074/mcp.M900223-MCP200

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Molecular & Cellular Proteomics 9: 225-241, 2010.

引用

页码：225 / 241

页数：17

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