The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries
Open accessAbstract
Quantitative phosphoproteomics has transformed investigations of cell signaling, but it remains challenging to scale the technology for high-throughput analyses. Here we report a rapid and reproducible approach to analyze hundreds of phosphoproteomes using data-independent acquisition (DIA) with an accurate site localization score incorporated into Spectronaut. DIA-based phosphoproteomics achieves an order of magnitude broader dynamic range, higher reproducibility of identification, and improved sensitivity and accuracy of quantification compared to state-of-the-art data-dependent acquisition (DDA)-based phosphoproteomics. Notably, direct DIA without the need of spectral libraries performs close to analyses using project-specific libraries, quantifying > 20,000 phosphopeptides in 15 min single-shot LC-MS analysis per condition. Adaptation of a 3D multiple regression model-based algorithm enables global determination of phosphorylation site stoichiometry in DIA. Scalability of the DIA approach is demonstrated by systematically analyzing the effects of thirty kinase inhibitors in context of epidermal growth factor (EGF) signaling showing that specific protein kinases mediate EGF-dependent phospho-regulation.
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Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
In silico prediction of protein-protein interactions in human macrophages
Souiai, O., Guerfali, F., Ben Miled, S., Brun, C., & Benkahla, A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-157 · Cited by 10,803
Significance analysis of microarrays applied to the ionizing radiation response
Tusher, V. G., Tibshirani, R., & Chu, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062498 · Cited by 10,568
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The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,500
Self-citationRappsilber, J., Mann, M., & Ishihama, Y. (2007) · Nature Protocols · doi:10.1038/nprot.2007.261 · Cited by 4,641
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., & Mann, M. (2006) · Cell · doi:10.1016/j.cell.2006.09.026 · Cited by 3,499
Self-citationThe Reactome Pathway Knowledgebase
Fabregat, A., Jupe, S., Matthews, L., Sidiropoulos, K., Gillespie, M., Garapati, P., Haw, R., Jassal, B., Korninger, F., May, B., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1132 · Cited by 2,855
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis
Olsen, J. V., Vermeulen, M., Santamaria, A., Kumar, C., Miller, M. L., Jensen, L. J., Gnad, F., Cox, J., Jensen, T. S., Nigg, E. A., et al. (2010) · Science Signaling · doi:10.1126/scisignal.2000475 · Cited by 1,479
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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts
Demichev, V., Szyrwiel, L., Yu, F., Teo, G. C., Rosenberger, G., Niewienda, A., Ludwig, D., Decker, J., Kaspar-Schoenefeld, S., Lilley, K. S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31492-0 · Cited by 441
Bekker-Jensen, D. B., Martínez-Val, A., Steigerwald, S., Rüther, P., Fort, K. L., Arrey, T. N., Harder, A., Makarov, A., & Olsen, J. V. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001906 · Cited by 425
Self-citationGuzman, U. H., Martinez-Val, A., Ye, Z., Damoc, E., Arrey, T. N., Pashkova, A., Renuse, S., Denisov, E., Petzoldt, J., Peterson, A. C., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02099-7 · Cited by 346
Self-citationAnalysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
Yu, F., Teo, G. C., Kong, A. T., Fröhlich, K., Li, G. X., Demichev, V., & Nesvizhskii, A. I. (2023) · Nature Communications · doi:10.1038/s41467-023-39869-5 · Cited by 292
Skowronek, P., Thielert, M., Voytik, E., Tanzer, M. C., Hansen, F. M., Willems, S., Karayel, O., Brunner, A.-D., Meier, F., & Mann, M. (2022) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100279 · Cited by 281
Metadata
- Authors
- Bekker-Jensen, D. B., Bernhardt, O. M., Hogrebe, A., Martinez-Val, A., Verbeke, L., Gandhi, T., Kelstrup, C. D., Reiter, L., & Olsen, J. V.
- Venue
- Nature Communications
- Published
- 2020-02-07
- Volume
- 11
- Issue
- 1
- Pages
- 787-787
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W3005045932
- Cited by
- 411
- References
- 36
- FWCI
- 20.48
- Type
- journal article
- Language
- en
- Open access
- gold
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- Bekker-Jensen, D. B., Bernhardt, O. M., Hogrebe, A., Martinez-Val, A., Verbeke, L., Gandhi, T., Kelstrup, C. D., Reiter, L., & Olsen, J. V. (2020). Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nature Communications. https://doi.org/10.1038/s41467-020-14609-1
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