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Nat Methods DOI:10.1038/nmeth.2763

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

Publication TypeJournal Article
Year of Publication2014
AuthorsKennedy, JJ, Abbatiello, SE, Kim, K, Yan, P, Whiteaker, JR, Lin, C, Kim, JSeok, Zhang, Y, Wang, X, Ivey, RG, Zhao, L, Min, H, Lee, Y, Yu, M-H, Yang, EGyeong, Lee, C, Wang, P, Rodriguez, H, Kim, Y, Carr, SA, Paulovich, AG
JournalNat Methods
Date Published2014 Feb
KeywordsBiological Assay, Biomarkers, Tumor, Breast Neoplasms, Chromatography, High Pressure Liquid, Electrophoresis, Gel, Two-Dimensional, Feasibility Studies, Female, Humans, Pilot Projects, Proteome, Proteomics, Survival Rate, Tandem Mass Spectrometry, Tumor Cells, Cultured

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.


Alternate JournalNat. Methods
PubMed ID24317253
PubMed Central IDPMC3922286
Grant ListU24 CA160034 / CA / NCI NIH HHS / United States
R01 GM082802 / GM / NIGMS NIH HHS / United States
P50 CA138293 / CA / NCI NIH HHS / United States
RC2CA148286 / CA / NCI NIH HHS / United States
RC2 CA148286 / CA / NCI NIH HHS / United States
U24CA160034 / CA / NCI NIH HHS / United States
P50CA138293 / CA / NCI NIH HHS / United States