The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule
Open accessAbstract
Most proteomics studies attempt to maximize the number of peptide identifications and subsequently infer proteins containing two or more peptides as reliable protein identifications. In this study, we evaluate the effect of this "two-peptide" rule on protein identifications, using multiple search tools and data sets. Contrary to the intuition, the "two-peptide" rule reduces the number of protein identifications in the target database more significantly than in the decoy database and results in increased false discovery rates, compared to the case when single-hit proteins are not discarded. We therefore recommend that the "two-peptide" rule should be abandoned, and instead, protein identifications should be subject to the estimation of error rates, as is the case with peptide identifications. We further extend the generating function approach (originally proposed for evaluating matches between a peptide and a single spectrum) to evaluating matches between a protein and an entire spectral data set.
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Cites
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Semi-supervised learning for peptide identification from shotgun proteomics datasets
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424
Lu, P., Vogel, C., Wang, R., Yao, X., & Marcotte, E. M. (2007) · Nature Biotechnology · doi:10.1038/nbt1270 · Cited by 1,139
Interpretation of Shotgun Proteomic Data
Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025
Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases
Käll, L., Storey, J. D., MacCoss, M. J., & Noble, W. S. (2008) · Journal of Proteome Research · doi:10.1021/pr700600n · Cited by 607
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
The, M., MacCoss, M. J., Noble, W. S., & Käll, L. (2016) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-016-1460-7 · Cited by 454
Proteogenomic Characterization of Human Early-Onset Gastric Cancer
Mun, D.-G., Bhin, J., Kim, S., Kim, H., Jung, J. H., Jung, Y., Jang, Y. E., Park, J. M., Kim, H., Jung, Y., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2018.12.003 · Cited by 294
Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A. I., Pedrioli, P. G. A., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4398 · Cited by 203
Cilento, E. M., Jin, L., Stewart, T., Shi, M., Sheng, L., & Zhang, J. (2019) · Journal of Neurochemistry · doi:10.1111/jnc.14635 · Cited by 60
Metadata
- Authors
- Gupta, N., & Pevzner, P. A.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-08-14
- Volume
- 8
- Issue
- 9
- Pages
- 4173-4181
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2064745516
- Cited by
- 186
- References
- 6
- FWCI
- 8.25
- Type
- journal article
- Language
- en
- Open access
- green
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