The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
A targeted proteomics–based pipeline for verification of biomarkers in plasma
Open accessAbstract
High-throughput technologies can now identify hundreds of candidate protein biomarkers for any disease with relative ease. However, because there are no assays for the majority of proteins and de novo immunoassay development is prohibitively expensive, few candidate biomarkers are tested in clinical studies. We tested whether the analytical performance of a biomarker identification pipeline based on targeted mass spectrometry would be sufficient for data-dependent prioritization of candidate biomarkers, de novo development of assays and multiplexed biomarker verification. We used a data-dependent triage process to prioritize a subset of putative plasma biomarkers from >1,000 candidates previously identified using a mouse model of breast cancer. Eighty-eight novel quantitative assays based on selected reaction monitoring mass spectrometry were developed, multiplexed and evaluated in 80 plasma samples. Thirty-six proteins were verified as being elevated in the plasma of tumor-bearing animals. The analytical performance of this pipeline suggests that it should support the use of an analogous approach with human samples.
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Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
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Protein biomarker discovery and validation: the long and uncertain path to clinical utility
Rifai, N., Gillette, M. A., & Carr, S. A. (2006) · Nature Biotechnology · doi:10.1038/nbt1235 · Cited by 1,867
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733
Selected reaction monitoring for quantitative proteomics: a tutorial
Lange, V., Picotti, P., Domon, B., & Aebersold, R. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.61 · Cited by 1,407
Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins
Anderson, L., & Hunter, C. L. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500331-mcp200 · Cited by 1,230
Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., & Pearson, T. W. (2004) · Journal of Proteome Research · doi:10.1021/pr034086h · Cited by 804
Keshishian, H., Addona, T., Burgess, M., Kuhn, E., & Carr, S. A. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700354-mcp200 · Cited by 684
Biological Variation: From Principles to Practice
Fraser, C. G. (2001) · Cited by 653
Bordeaux, J., Welsh, A. W., Agarwal, S., Killiam, E., Baquero, M. T., Hanna, J. A., Anagnostou, V. K., & Rimm, D. L. (2010) · BioTechniques · doi:10.2144/000113382 · Cited by 589
The Clinical Plasma Proteome: A Survey of Clinical Assays for Proteins in Plasma and Serum
Anderson, N. L. (2010) · Clinical Chemistry · doi:10.1373/clinchem.2009.126706 · Cited by 562
Cited by
Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., & Coon, J. J. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.020131 · Cited by 1,288
Revisiting biomarker discovery by plasma proteomics
Geyer, P. E., Holdt, L. M., Teupser, D., & Mann, M. (2017) · Molecular Systems Biology · doi:10.15252/msb.20156297 · Cited by 917
Next-generation proteomics: towards an integrative view of proteome dynamics
Altelaar, A. F. M., Munoz, J., & Heck, A. J. R. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3356 · Cited by 782
Using i RT, a normalized retention time for more targeted measurement of peptides
Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J., MacCoss, M. J., & Rinner, O. (2012) · PROTEOMICS · doi:10.1002/pmic.201100463 · Cited by 600
Carr, S. A., Abbatiello, S. E., Ackermann, B. L., Borchers, C., Domon, B., Deutsch, E. W., Grant, R. P., Hoofnagle, A. N., Hüttenhain, R., Koomen, J. M., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.036095 · Cited by 561
Self-citation
Metadata
- Authors
- Whiteaker, J. R., Lin, C., Kennedy, J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U. J., Kelly-Spratt, K. S., Krasnoselsky, A., Gafken, P. R., Hogan, J. M., Jones, L. A., Wang, P., Amon, L., Chodosh, L. A., Nelson, P. S., McIntosh, M. W., Kemp, C. J., & Paulovich, A. G.
- Venue
- Nature Biotechnology
- Published
- 2011-06-19
- Volume
- 29
- Issue
- 7
- Pages
- 625-634
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1964753682
- Cited by
- 364
- References
- 44
- FWCI
- 22.02
- Type
- journal article
- Language
- en
- Open access
- green
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- Whiteaker, J. R., Lin, C., Kennedy, J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U. J., Kelly-Spratt, K. S., Krasnoselsky, A., Gafken, P. R., Hogan, J. M., Jones, L. A., Wang, P., Amon, L., Chodosh, L. A., Nelson, P. S., . . . Paulovich, A. G. (2011). A targeted proteomics–based pipeline for verification of biomarkers in plasma. Nature Biotechnology. https://doi.org/10.1038/nbt.1900
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