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Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome
Abstract
High-efficiency nanoscale reversed-phase liquid chromatography (chromatographic peak capacities of approximately 1000: Shen, Y.; Zhao, R.; Berger, S. J.; Anderson, G. A.; Rodriguez, N.; Smith, R. D. Anal. Chem. 2002, 74, 4235. Shen, Y.; Moore, R. J.; Zhao, R.; Blonder, J.; Auberry, D. L.; Masselon, C.; Pasa-Tolic, L.; Hixson, K. K.; Auberry, K. J.; Smith, R. D. Anal. Chem. 2003, 75, 3596.) and strong cation exchange LC was used to obtain ultra-high-efficiency separations (combined chromatographic peak capacities of >10(4)) in conjunction with tandem mass spectrometry (MS/MS) for characterization of the human plasma proteome. Using conservative SEQUEST peptide identification criteria (i.e., without considering chymotryptic or elastic peptides) and peptide LC normalized elution time constraints, the separation quality enabled the identification of proteins over a dynamic range of greater than 8 orders of magnitude in relative abundance using ion trap MS/MS instrumentation. Between 800 and 1682 human proteins were identified, depending on the criteria used for identification, from a total of 365 microg of human plasma. The analyses identified relatively low-level (approximately pg/mL) proteins (e.g., cytokines) coexisting with high-abundance proteins (e.g., mg/mL-level serum albumin).
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Cites
Anderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Cited by
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
Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
Proteomics by Mass Spectrometry: Approaches, Advances, and Applications
Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-061008-124934 · Cited by 1,078
Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., et al. (2005) · PROTEOMICS · doi:10.1002/pmic.200500358 · Cited by 787
A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas
Farrah, T., Deutsch, E. W., Omenn, G. S., Campbell, D. S., Sun, Z., Bletz, J. A., Mallick, P., Katz, J. E., Malmström, J., Ossola, R., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.006353 · Cited by 451
Metadata
- Authors
- Shen, Y., Jacobs, J. M., Camp, D. G., Fang, R., Moore, R. J., Smith, R. D., Xiao, W., Davis, R. W., & Tompkins, R. G.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2004-01-13
- Volume
- 76
- Issue
- 4
- Pages
- 1134-1144
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2044970750
- Cited by
- 297
- References
- 2
- FWCI
- 16.61
- Type
- journal article
- Language
- en
- Open access
- closed
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- The paper
- Shen, Y., Jacobs, J. M., Camp, D. G., Fang, R., Moore, R. J., Smith, R. D., Xiao, W., Davis, R. W., & Tompkins, R. G. (2004). Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome. Analytical Chemistry. https://doi.org/10.1021/ac034869m
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