Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses
Open accessAbstract
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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A high degree of reproducibility is difficult to achieve for complex samples in DDA.
“In general, these studies confirmed that a high degree of reproducibility is difficult to achieve for complex samples10.”
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- Authors
- Rudnick, P. A., Clauser, K. R., Kilpatrick, L. E., Tchekhovskoi, D. V., Neta, P., Blonder, N., Billheimer, D. D., Blackman, R. K., Bunk, D. M., Cardasis, H. L., Ham, A.-J. L., Jaffe, J. D., Kinsinger, C. R., Mesri, M., Neubert, T. A., Schilling, B., Tabb, D. L., Tegeler, T. J., Vega-Montoto, L., Variyath, A. M., Wang, M., Wang, P., Whiteaker, J. R., Zimmerman, L. J., Carr, S. A., Fisher, S. J., Gibson, B. W., Paulovich, A. G., Regnier, F. E., Rodriguez, H., Spiegelman, C., Tempst, P., Liebler, D. C., & Stein, S. E.
- Affiliations
- National Institute of Standards and Technology (US)
- Broad Institute (US)
- University of Arizona (US)
- New York University (US)
- Vanderbilt University (US)
- National Institutes of Health (US)
- Buck Institute for Research on Aging (US)
- Texas A&M University (US)
- Fred Hutch Cancer Center (US)
- University of California, San Francisco (US)
- Purdue University West Lafayette (US)
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- Liebler, Daniel C.
- Stein, Stephen E.
- ORCID
- Rudnick, Paul A.
- Clauser, Karl R.
- Kilpatrick, Lisa E.
- Tchekhovskoi, Dmitrii V.
- Blonder, Nikša
- Billheimer, Dean D.
- Bunk, David M.
- Ham, Amy-Joan L.
- Jaffe, Jacob D.
- Kinsinger, Christopher R.
- Mesri, Mehdi
- Neubert, Thomas A.
- Schilling, Birgit
- Tabb, David L.
- Variyath, Asokan Mulayath
- Wang, Mu
- Wang, Pei
- Whiteaker, Jeffrey R.
- Zimmerman, Lisa J.
- Carr, Steven A.
- Fisher, Susan J.
- Gibson, Bradford W.
- Paulovich, Amanda G.
- Regnier, Fred E.
- Rodriguez, Henry
- Tempst, Paul
- Liebler, Daniel C.
- Stein, Stephen E.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2010-02
- Volume
- 9
- Issue
- 2
- Pages
- 225-241
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC2830836
- OpenAlex
- W2012913476
- Cited by
- 183
- References
- 28
- Citations by year
- 2026: 6 · 2025: 6 · 2024: 6 · 2023: 5 · 2022: 6 · 2021: 4 · 2020: 4 · 2019: 10 · 2018: 9 · 2017: 10 · 2016: 13 · 2015: 13 · 2014: 20 · 2013: 17 · 2012: 18
- FWCI
- 7.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Massachusetts General Hospital
- Purdue University
- Vanderbilt University
- Memorial Sloan-Kettering Cancer Center
- University of Washington
- University of Arizona
- Indiana University-Purdue University Indianapolis
- University of Victoria
- Broad Institute
- Buck Institute for Research on Aging
- York University
- University of British Columbia
- National Institutes of Health
- National Institute of Standards and Technology
- School of Medicine, Vanderbilt University
- University of North Carolina at Chapel Hill
- University of California, San Francisco
- National Cancer Institute (U24CA126480, U24CA126485, U24CA126477, U24CA126479, U24CA126476)
- Lawrence Berkeley National Laboratory
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- quality assessment, technical variability, chromatographic performance, peptide identification, inter-laboratory variability, outlier detection, proteomics
- MeSH terms
- Animals, Chickens, Chromatography, Liquid, Egg Proteins, Laboratories, Saccharomyces cerevisiae, Software, Reproducibility of Results, Proteome, Saccharomyces cerevisiae Proteins, Proteomics, Tandem Mass Spectrometry
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