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Molecular & cellular proteomics : MCP DOI:10.1074/mcp.M111.013854

Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.

Publication TypeJournal Article
Year of Publication2011
AuthorsKuhn, E, Whiteaker, JR, Mani, DR, Jackson, AM, Zhao, L, Pope, ME, Smith, D, Rivera, KD, Anderson, NL, Skates, SJ, Pearson, TW, Paulovich, AG, Carr, SA
JournalMolecular & cellular proteomics : MCP
Date Published2011/12/22

The inability to quantify large numbers of proteins in tissues and biofluids with high precision, sensitivity and throughput is a major bottleneck in biomarker studies. We previously demonstrated that coupling immunoaffinity enrichment using anti-peptide antibodies (SISCAPA) to MRM-MS produces immuno-MRM assays that can be multiplexed to quantify proteins in plasma with high sensitivity, specificity, and precision. Here we report the first systematic evaluation of the inter-laboratory performance of multiplexed (8-plex) immuno-MRM-MS in three independent labs. A staged study was carried out in which the effect of each processing and analysis step on assay CV, LOD, LOQ and recovery was evaluated. Limits of detection were at or below 1 ng/mL for the assayed proteins in 30 uL of plasma. Assay reproducibility was acceptable for verification studies, with median intra- and inter-laboratory CVs above the LOQ of 11% and <14%, respectively, for the entire immuno-MRM-MS assay process, including enzymatic digestion of plasma. Trypsin digestion and its requisite sample handling contributed the most to assay variability and reduced the recovery of target peptides from digested proteins. Using a stable isotope labeled protein as an internal standard instead of stable isotope labeled peptides to account for losses in the digestion process nearly doubled assay accuracy for this while improving assay precision 5%. Our results demonstrate that multiplexed immuno-MRM-MS can be made reproducible across independent laboratories and has the potential to be adopted widely for assaying proteins in matrices as complex as plasma.