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Mol Cell Proteomics DOI:10.1074/mcp.M112.027078

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Publication TypeJournal Article
Year of Publication2013
AuthorsAbbatiello, SE, Mani, DR, Schilling, B, MacLean, B, Zimmerman, LJ, Feng, X, Cusack, MP, Sedransk, N, Hall, SC, Addona, T, Allen, S, Dodder, NG, Ghosh, M, Held, JM, Hedrick, V, H Inerowicz, D, Jackson, A, Keshishian, H, Kim, JWon, Lyssand, JS, C Riley, P, Rudnick, P, Sadowski, P, Shaddox, K, Smith, D, Tomazela, D, Wahlander, A, Waldemarson, S, Whitwell, CA, You, J, Zhang, S, Kinsinger, CR, Mesri, M, Rodriguez, H, Borchers, CH, Buck, C, Fisher, SJ, Gibson, BW, Liebler, D, MacCoss, M, Neubert, TA, Paulovich, A, Regnier, F, Skates, SJ, Tempst, P, Wang, M, Carr, SA
JournalMol Cell Proteomics
Date Published2013 Sep
KeywordsAmino Acid Sequence, Animals, Cattle, Chromatography, Liquid, Limit of Detection, Mass Spectrometry, Molecular Sequence Data, Peptides, Reference Standards, Software, Time Factors

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation


Alternate JournalMol. Cell Proteomics
PubMed ID23689285
PubMed Central IDPMC3769335
Grant ListU24 CA160034 / CA / NCI NIH HHS / United States
U24 CA126485 / CA / NCI NIH HHS / United States
R01 GM103551 / GM / NIGMS NIH HHS / United States
U24 126479 / / PHS HHS / United States
U24 126480 / / PHS HHS / United States
S10 RR0021222. / RR / NCRR NIH HHS / United States
R01 GM107142 / GM / NIGMS NIH HHS / United States
U24 CA126476 / CA / NCI NIH HHS / United States
U24 126477 / / PHS HHS / United States
S10 RR021222 / RR / NCRR NIH HHS / United States