The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Decision tree–driven tandem mass spectrometry for shotgun proteomics
Open accessAbstract
Mass spectrometry has become a key technology for modern large-scale protein sequencing. Tandem mass spectrometry, the process of peptide ion dissociation followed by mass-to-charge ratio (m/z) analysis, is the critical component for peptide identification. Recent advances in mass spectrometry now permit two discrete, and complementary, types of peptide ion fragmentation: collision-activated dissociation (CAD) and electron transfer dissociation (ETD) on a single instrument. To exploit this complementarity and increase sequencing success rates, we designed and embedded a data-dependent decision tree algorithm (DT) to make unsupervised, real-time decisions of which fragmentation method to use based on precursor charge and m/z. Applying the DT to large-scale proteome analyses of Saccharomyces cerevisiae and human embryonic stem cells, we identified 53,055 peptides in total, which was greater than by using CAD (38,293) or ETD (39,507) alone. In addition, the DT method also identified 7,422 phosphopeptides, compared to either 2,801 (CAD) or 5,874 (ETD) phosphopeptides.
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Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Peptide 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
Self-citationLarge-scale phosphorylation analysis of mouse liver
Villén, J., Beausoleil, S. A., Gerber, S. A., & Gygi, S. P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609836104 · Cited by 730
Protein identification using sequential ion/ion reactions and tandem mass spectrometry
Coon, J. J., Ueberheide, B., Syka, J. E. P., Dryhurst, D. D., Ausio, J., Shabanowitz, J., & Hunt, D. F. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503189102 · Cited by 373
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Cited by
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
Exosomes: proteomic insights and diagnostic potential
Simpson, R. J., Lim, J. W., Moritz, R. L., & Mathivanan, S. (2009) · Expert Review of Proteomics · doi:10.1586/epr.09.17 · Cited by 1,108
MS-GF+ makes progress towards a universal database search tool for proteomics
Kim, S., & Pevzner, P. A. (2014) · Nature Communications · doi:10.1038/ncomms6277 · Cited by 1,098
Wnt Signaling through Inhibition of β-Catenin Degradation in an Intact Axin1 Complex
Li, V. S. W., Ng, S. S., Boersema, P. J., Low, T. Y., Karthaus, W. R., Gerlach, J. P., Mohammed, S., Heck, A. J. R., Maurice, M. M., Mahmoudi, T., et al. (2012) · Cell · doi:10.1016/j.cell.2012.05.002 · Cited by 889
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801
Metadata
- Authors
- Swaney, D. L., McAlister, G. C., & Coon, J. J.
- Venue
- Nature Methods
- Published
- 2008-10-19
- Volume
- 5
- Issue
- 11
- Pages
- 959-964
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2062406929
- Cited by
- 312
- References
- 4
- FWCI
- 13.72
- Type
- journal article
- Language
- en
- Open access
- green
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