Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins
Open accessAbstract
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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CPTAC and associated projects focused on targeted proteomics via SRM represent the most advanced work on robustness and transferability of quantitative proteomics methods to date.
“Finally, a further comparison with CPTAC and associated projects focused on targeted proteomics via SRM is of interest as it represents the most advanced work on the robustness and transferability of quantitative proteomics methods to date24, 26, 27.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [27]
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References 60 · Cited by 184
- Authors
- Kennedy, J. J., Abbatiello, S. E., Kim, K., Yan, P., Whiteaker, J. R., Lin, C., Kim, J. S., Zhang, Y., Wang, X., Ivey, R. G., Zhao, L., Min, H., Lee, Y., Yu, M.-H., Yang, E. G., Lee, C., Wang, P., Rodriguez, H., Kim, Y., Carr, S. A., & Paulovich, A. G.
- Affiliations
- Fred Hutch Cancer Center (US)
- Broad Institute (US)
- Seoul National University (KR)
- Korea Institute of Science and Technology (KR)
- National Institutes of Health (US)
- Corresponding author
- Paulovich, Amanda G
- ORCID
- Venue
- Nature Methods
- Published
- 2013-12-08
- Volume
- 11
- Issue
- 2
- Pages
- 149-155
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3922286
- OpenAlex
- W2023720096
- Cited by
- 184
- References
- 60
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 8 · 2023: 8 · 2022: 10 · 2021: 15 · 2020: 11 · 2019: 11 · 2018: 14 · 2017: 26 · 2016: 31 · 2015: 31 · 2014: 12
- FWCI
- 11.06
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (P50CA138293, RC2CA148286, U24CA160034)
- National Institute of General Medical Sciences (R01GM082802)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- multiple reaction monitoring, assay standardization, breast cancer cell lines, molecular subtypes, tumor proteome, interlaboratory validation
- MeSH terms
- Biological Assay, Breast Neoplasms, Chromatography, High Pressure Liquid, Feasibility Studies, Female, Humans, Pilot Projects, Tumor Cells, Cultured, Biomarkers, Tumor, Electrophoresis, Gel, Two-Dimensional, Survival Rate, Proteome, Proteomics, Tandem Mass Spectrometry
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