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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.

SUBMITTER: Rudnick PA 

PROVIDER: S-EPMC2830836 | biostudies-other | 2010 Feb

REPOSITORIES: biostudies-other

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

Rudnick Paul A PA   Clauser Karl R KR   Kilpatrick Lisa E LE   Tchekhovskoi Dmitrii V DV   Neta Pedatsur P   Blonder Niksa N   Billheimer Dean D DD   Blackman Ronald K RK   Bunk David M DM   Cardasis Helene L HL   Ham Amy-Joan L AJ   Jaffe Jacob D JD   Kinsinger Christopher R CR   Mesri Mehdi M   Neubert Thomas A TA   Schilling Birgit B   Tabb David L DL   Tegeler Tony J TJ   Vega-Montoto Lorenzo L   Variyath Asokan Mulayath AM   Wang Mu M   Wang Pei P   Whiteaker Jeffrey R JR   Zimmerman Lisa J LJ   Carr Steven A SA   Fisher Susan J SJ   Gibson Bradford W BW   Paulovich Amanda G AG   Regnier Fred E FE   Rodriguez Henry H   Spiegelman Cliff C   Tempst Paul P   Liebler Daniel C DC   Stein Stephen E SE  

Molecular & cellular proteomics : MCP 20091016 2


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 p  ...[more]

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