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Mol Cell Proteomics DOI:10.1074/mcp.M114.047050

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.

Publication TypeJournal Article
Year of Publication2015
AuthorsAbbatiello, SE, Schilling, B, Mani, DR, Zimmerman, LJ, Hall, SC, MacLean, B, Albertolle, M, Allen, S, Burgess, M, Cusack, MP, Gosh, M, Hedrick, V, Held, JM, H Inerowicz, D, Jackson, A, Keshishian, H, Kinsinger, CR, Lyssand, J, Makowski, L, Mesri, M, Rodriguez, H, Rudnick, P, Sadowski, P, Sedransk, N, Shaddox, K, Skates, SJ, Kuhn, E, Smith, D, Whiteaker, JR, Whitwell, C, Zhang, S, Borchers, CH, Fisher, SJ, Gibson, BW, Liebler, DC, MacCoss, MJ, Neubert, TA, Paulovich, AG, Regnier, FE, Tempst, P, Carr, SA
JournalMol Cell Proteomics
Date Published2015 Sep
KeywordsChromatography, Liquid, Humans, Isotope Labeling, Mass Spectrometry, Neoplasm Proteins, Neoplasms, Peptides, Proteomics, Reproducibility of Results

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was


Alternate JournalMol. Cell Proteomics
PubMed ID25693799
PubMed Central IDPMC4563721
Grant ListU24 CA160034 / CA / NCI NIH HHS / United States
P30 CA016087 / CA / NCI NIH HHS / United States
U24 CA126485 / CA / NCI NIH HHS / United States
U24 CA159988 / CA / NCI NIH HHS / United States
U24CA159988 / 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 RR027953 / RR / NCRR NIH HHS / United States
P30 CA008748 / CA / NCI NIH HHS / United States
U24 CA126476 / CA / NCI NIH HHS / United States
U24 126477 / / PHS HHS / United States
U24CA160034 / CA / NCI NIH HHS / United States
S10 RR024604 / RR / NCRR NIH HHS / United States