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Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8.

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.

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Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Republic of Korea.
Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea.
Office of Cancer Clinical Proteomics Research, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA.


Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analytes in a panel of breast cancer-related cell lines. The median assay precision was 5.4%, with high interlaboratory correlation (R(2) > 0.96). Peptide measurements in breast cancer cell lines were able to discriminate among molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a large-scale effort to develop an MRM assay resource.

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