The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation
Open accessAbstract
Mass spectrometry (MS)-based proteomics now enables the analysis of thousands of phosphorylation sites in single projects. Among a wide range of analytical approaches, the combination of high resolution MS scans in an Orbitrap analyzer with low resolution MS/MS scans in a linear ion trap has proven to be particularly successful ("high-low" strategy). Here we investigate if the improved sensitivity of higher energy collisional dissociation (HCD) on an LTQ-Orbitrap Velos instrument allows a "high-high" strategy. A high resolution MS scan was followed by up to 10 HCD MS/MS scans, and we achieved cycle times of about 3 s making the method compatible with chromatographic time scales. Fragment mass accuracy increased about 50-fold compared to the "high-low" strategy. Unexpectedly, the HCD approach mapped up to 16,000 total phosphorylation sites in one day's measuring time--the same or better than the standard high-low strategy. Reducing the target values from a standard of 30,000 to 5000 ions did not severely affect identification rates but did decrease identification and localization scores for phosphorylation sites. We conclude that HCD in the new configuration is now a viable method for large-scale phosphoproteome analysis alongside collisional induced dissociation, (CID) and electron capture/transfer dissociation (ECD/ETD).
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Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
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Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352
Self-citationPeptide and protein sequence analysis by electron transfer dissociation mass spectrometry
Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., & Hunt, D. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402700101 · Cited by 2,370
A dual pressure linear ion trap orbitrap instrument with very high sequencing speed
Olsen, J. V., Schwartz, J. C., Griep-Raming, J., Nielsen, M. L., Damoc, E., Denisov, E., Lange, O., Remes, P., Taylor, D., Splendore, M., et al. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900375-mcp200 · Cited by 464
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Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
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Olsen, J. V., & Mann, M. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.034181 · Cited by 591
Self-citationToward a comprehensive characterization of a human cancer cell phosphoproteome
Zhou, H., Di Palma, S., Preisinger, C., Peng, M., Polat, A. N., Heck, A. J. R., & Mohammed, S. (2013) · Journal of Proteome Research · doi:10.1021/pr300630k · Cited by 438
Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues
Lundby, A., Secher, A., Lage, K., Nordsborg, N. B., Dmytriyev, A., Lundby, C., & Olsen, J. V. (2012) · Nature Communications · doi:10.1038/ncomms1871 · Cited by 343
Self-citationIlluminating the dark phosphoproteome
Needham, E. J., Parker, B. L., Burykin, T., James, D. E., & Humphrey, S. J. (2019) · Science Signaling · doi:10.1126/scisignal.aau8645 · Cited by 334
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Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265
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Doll, S., & Burlingame, A. L. (2015) · ACS Chemical Biology · doi:10.1021/cb500904b · Cited by 261
Zhu, G., Sun, L., Yan, X., & Dovichi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac303750g · Cited by 103
Metadata
- Authors
- Nagaraj, N., D’Souza, R. C. J., Cox, J., Olsen, J. V., & Mann, M.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-10-26
- Volume
- 9
- Issue
- 12
- Pages
- 6786-6794
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2018247248
- Cited by
- 163
- References
- 4
- FWCI
- 10.64
- Type
- journal article
- Language
- en
- Open access
- green
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