Article

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

National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
Molecular &amp Cellular Proteomics (impact factor: 7.4). 10/2009; 9(2):225-41. DOI:10.1074/mcp.M900223-MCP200 pp.225-41
Source: PubMed

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.

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Keywords

46 system performance metrics
 
data sets
 
electrospray source stability
 
interlaboratory studies
 
interlaboratory variation
 
LC-MS/MS analytical applications
 
LC-MS/MS-based proteomics analyses
 
metrics enables rational
 
monitoring chromatographic performance
 
MS2 signals
 
outlier data
 
peptide identification
 
quantitative assessment
 
quantitative quality assessment
 
reasonable responses
 
replicate LC-MS/MS analyses
 
subtle differences
 
system components
 
system performance
 
technical variability